Homework 1 by Smutin Daniil

Prepare data

data("BCI")
data("BCI.env")
BCI
##    Abarema.macradenia Vachellia.melanoceras Acalypha.diversifolia
## 1                   0                     0                     0
## 2                   0                     0                     0
## 3                   0                     0                     0
## 4                   0                     0                     0
## 5                   0                     0                     0
## 6                   0                     0                     0
## 7                   0                     0                     0
## 8                   0                     0                     0
## 9                   0                     0                     0
## 10                  1                     0                     0
## 11                  0                     0                     0
## 12                  0                     0                     0
## 13                  0                     0                     0
## 14                  0                     0                     0
## 15                  0                     0                     0
## 16                  0                     0                     0
## 17                  0                     0                     0
## 18                  0                     0                     0
## 19                  0                     0                     0
## 20                  0                     0                     0
## 21                  0                     0                     0
## 22                  0                     0                     0
## 23                  0                     0                     0
## 24                  0                     0                     0
## 25                  0                     0                     0
## 26                  0                     0                     0
## 27                  0                     0                     0
## 28                  0                     2                     0
## 29                  0                     0                     0
## 30                  0                     0                     0
## 31                  0                     0                     0
## 32                  0                     1                     0
## 33                  0                     0                     0
## 34                  0                     0                     1
## 35                  0                     0                     0
## 36                  0                     0                     0
## 37                  0                     0                     0
## 38                  0                     0                     0
## 39                  0                     0                     0
## 40                  0                     0                     1
## 41                  0                     0                     0
## 42                  0                     0                     0
## 43                  0                     0                     0
## 44                  0                     0                     0
## 45                  0                     0                     0
## 46                  0                     0                     0
## 47                  0                     0                     0
## 48                  0                     0                     0
## 49                  0                     0                     0
## 50                  0                     0                     0
##    Acalypha.macrostachya Adelia.triloba Aegiphila.panamensis
## 1                      0              0                    0
## 2                      0              0                    0
## 3                      0              0                    0
## 4                      0              3                    0
## 5                      0              1                    1
## 6                      0              0                    0
## 7                      0              0                    1
## 8                      0              0                    0
## 9                      0              5                    0
## 10                     0              0                    1
## 11                     0              0                    0
## 12                     0              1                    1
## 13                     0              1                    1
## 14                     0              0                    0
## 15                     0              2                    0
## 16                     0              2                    0
## 17                     0              0                    1
## 18                     0              1                    1
## 19                     0              0                    1
## 20                     0              0                    2
## 21                     0              0                    1
## 22                     0              1                    0
## 23                     0              0                    0
## 24                     0              2                    1
## 25                     0              0                    1
## 26                     0              0                    0
## 27                     0              1                    4
## 28                     1              0                    1
## 29                     0              1                    0
## 30                     0             14                    2
## 31                     0              5                    0
## 32                     0              7                    0
## 33                     0              3                    1
## 34                     0              3                    0
## 35                     0              6                    0
## 36                     0              1                    0
## 37                     0              2                    0
## 38                     0              6                    0
## 39                     0              9                    0
## 40                     0              7                    0
## 41                     0              0                    1
## 42                     0              0                    0
## 43                     0              0                    1
## 44                     0              4                    0
## 45                     0              0                    0
## 46                     0              0                    0
## 47                     0              2                    0
## 48                     0              1                    0
## 49                     0              0                    0
## 50                     0              1                    0
##    Alchornea.costaricensis Alchornea.latifolia Alibertia.edulis
## 1                        2                   0                0
## 2                        1                   0                0
## 3                        2                   0                0
## 4                       18                   0                0
## 5                        3                   0                0
## 6                        2                   1                0
## 7                        0                   0                0
## 8                        2                   0                0
## 9                        2                   0                0
## 10                       2                   0                0
## 11                      10                   0                0
## 12                       3                   0                0
## 13                       1                   0                1
## 14                       4                   0                0
## 15                       2                   0                0
## 16                       2                   0                0
## 17                       2                   0                0
## 18                       0                   0                0
## 19                       1                   0                0
## 20                       2                   0                0
## 21                       2                   0                0
## 22                       4                   0                0
## 23                       1                   0                0
## 24                       0                   0                0
## 25                       2                   0                0
## 26                       3                   0                0
## 27                       3                   0                0
## 28                       2                   0                0
## 29                       1                   0                0
## 30                       6                   0                0
## 31                       4                   0                0
## 32                       6                   0                0
## 33                       3                   0                0
## 34                       5                   0                0
## 35                       8                   0                0
## 36                       3                   0                0
## 37                       4                   0                0
## 38                       2                   0                0
## 39                       3                   0                0
## 40                       3                   0                0
## 41                      11                   0                0
## 42                       0                   0                0
## 43                       3                   0                0
## 44                       4                   0                0
## 45                       0                   0                0
## 46                       0                   0                0
## 47                       1                   0                0
## 48                       3                   0                0
## 49                       6                   0                0
## 50                       2                   0                0
##    Allophylus.psilospermus Alseis.blackiana Amaioua.corymbosa
## 1                        0               25                 0
## 2                        0               26                 0
## 3                        0               18                 0
## 4                        0               23                 0
## 5                        1               16                 0
## 6                        0               14                 0
## 7                        0               18                 0
## 8                        0               14                 0
## 9                        0               16                 0
## 10                       0               14                 0
## 11                       0               14                 0
## 12                       2               19                 0
## 13                       1                8                 0
## 14                       0               17                 0
## 15                       0               15                 0
## 16                       3               25                 0
## 17                       2               31                 0
## 18                       0                7                 0
## 19                       1               13                 0
## 20                       0               10                 0
## 21                       1               12                 0
## 22                       4               22                 0
## 23                       0                5                 0
## 24                       1               14                 0
## 25                       0               20                 0
## 26                       0                7                 0
## 27                       3               17                 0
## 28                       0               16                 0
## 29                       0               15                 0
## 30                       0               36                 0
## 31                       0               11                 0
## 32                       0               21                 0
## 33                       1               24                 0
## 34                       0               42                 0
## 35                       0               93                 0
## 36                       0                8                 0
## 37                       0               19                 0
## 38                       1               25                 0
## 39                       1               38                 0
## 40                       1               65                 0
## 41                       0               13                 0
## 42                       0               13                 0
## 43                       0                8                 0
## 44                       0               13                 0
## 45                       0               10                 0
## 46                       0               29                 2
## 47                       1               17                 0
## 48                       1               12                 0
## 49                       1                6                 1
## 50                       1                9                 0
##    Anacardium.excelsum Andira.inermis Annona.spraguei Apeiba.glabra
## 1                    0              0               1            13
## 2                    0              0               0            12
## 3                    0              0               1             6
## 4                    0              0               0             3
## 5                    0              1               0             4
## 6                    0              1               0            10
## 7                    0              0               0             5
## 8                    1              0               1             4
## 9                    0              1               1             5
## 10                   0              0               0             5
## 11                   1              1               0             2
## 12                   0              0               0             4
## 13                   0              0               3             1
## 14                   0              1               4             5
## 15                   0              0               2             8
## 16                   0              0               0             5
## 17                   0              0               1             1
## 18                   2              0               2             1
## 19                   0              2               1            13
## 20                   0              0               2             6
## 21                   2              0               0             2
## 22                   0              1               0             7
## 23                   2              1               0             3
## 24                   1              2               0             6
## 25                   1              0               0             6
## 26                   0              2               0             4
## 27                   0              0               0             2
## 28                   2              1               0             6
## 29                   0              1               0             5
## 30                   0              2               0             5
## 31                   0              0               0             5
## 32                   0              0               0             4
## 33                   0              2               0             8
## 34                   0              1               0             3
## 35                   0              0               0             5
## 36                   0              0               1             3
## 37                   0              0               0             4
## 38                   0              0               1             1
## 39                   0              0               0             3
## 40                   2              0               0             7
## 41                   2              1               0             2
## 42                   0              1               0             5
## 43                   0              2               0             2
## 44                   0              0               0             7
## 45                   0              0               0             1
## 46                   0              0               3             0
## 47                   0              0               1             8
## 48                   3              1               2             2
## 49                   1              2               0             4
## 50                   2              1               0             3
##    Apeiba.tibourbou Aspidosperma.desmanthum Astrocaryum.standleyanum
## 1                 2                       0                        0
## 2                 0                       0                        2
## 3                 1                       0                        1
## 4                 1                       1                        5
## 5                 0                       1                        6
## 6                 0                       1                        2
## 7                 0                       0                        2
## 8                 1                       0                        0
## 9                 0                       0                        2
## 10                0                       1                        1
## 11                0                       0                        3
## 12                0                       0                        1
## 13                1                       0                       12
## 14                1                       1                        5
## 15                0                       0                        0
## 16                0                       0                        5
## 17                0                       1                        1
## 18                1                       0                        6
## 19                1                       0                        2
## 20                1                       0                        0
## 21                0                       2                        3
## 22                0                       0                        8
## 23                0                       0                       17
## 24                0                       0                        7
## 25                0                       3                       13
## 26                1                       0                        4
## 27                0                       0                        5
## 28                0                       2                        4
## 29                0                       2                        1
## 30                1                       0                        1
## 31                0                       0                        3
## 32                0                       1                        4
## 33                1                       3                       10
## 34                1                       3                        3
## 35                1                       0                        3
## 36                0                       3                        2
## 37                0                       1                        2
## 38                0                       3                        1
## 39                0                       5                        1
## 40                0                       3                        3
## 41                0                       0                        3
## 42                1                       2                       13
## 43                0                       3                        1
## 44                0                       2                        6
## 45                0                       0                        1
## 46                3                       1                        6
## 47                1                       2                        5
## 48                0                       2                        7
## 49                0                       1                        4
## 50                1                       2                        4
##    Astronium.graveolens Attalea.butyracea Banara.guianensis
## 1                     6                 0                 0
## 2                     0                 1                 0
## 3                     1                 0                 0
## 4                     3                 0                 0
## 5                     0                 0                 0
## 6                     1                 1                 0
## 7                     2                 1                 0
## 8                     2                 0                 0
## 9                     0                 0                 0
## 10                    0                 0                 0
## 11                    0                 0                 0
## 12                    0                 0                 0
## 13                    0                 4                 0
## 14                    0                 4                 0
## 15                    0                 0                 0
## 16                    0                 1                 0
## 17                    2                 0                 0
## 18                    0                 2                 0
## 19                    0                 0                 0
## 20                    0                 0                 0
## 21                    1                 1                 0
## 22                    2                 1                 0
## 23                    0                 1                 1
## 24                    0                 1                 0
## 25                    0                 2                 0
## 26                    2                 2                 0
## 27                    0                 1                 0
## 28                    1                 0                 0
## 29                    1                 0                 0
## 30                    1                 0                 0
## 31                    1                 2                 0
## 32                    0                 0                 0
## 33                    1                 0                 0
## 34                    7                 0                 0
## 35                    1                 0                 0
## 36                    0                 0                 0
## 37                    0                 0                 0
## 38                    0                 1                 0
## 39                    2                 0                 0
## 40                    1                 0                 0
## 41                    0                 1                 0
## 42                    0                 1                 0
## 43                    0                 0                 0
## 44                    0                 0                 0
## 45                    0                 1                 0
## 46                    1                 1                 0
## 47                    0                 0                 0
## 48                    0                 2                 0
## 49                    0                 1                 0
## 50                    0                 0                 0
##    Beilschmiedia.pendula Brosimum.alicastrum Brosimum.guianense
## 1                      4                   5                  0
## 2                      5                   2                  0
## 3                      7                   4                  0
## 4                      5                   3                  0
## 5                      8                   2                  0
## 6                      6                   2                  0
## 7                      5                   6                  0
## 8                      9                   4                  0
## 9                     11                   3                  0
## 10                    14                   6                  0
## 11                     1                   5                  0
## 12                     2                   4                  0
## 13                     0                   2                  0
## 14                     3                   4                  0
## 15                     9                   3                  0
## 16                     4                   4                  0
## 17                     2                   5                  0
## 18                     0                   0                  0
## 19                     2                   4                  0
## 20                     1                   0                  0
## 21                     2                   2                  0
## 22                     0                   8                  0
## 23                     0                   2                  0
## 24                    16                   4                  0
## 25                     5                   5                  0
## 26                     3                   3                  0
## 27                     1                   5                  0
## 28                     3                   4                  0
## 29                    11                   2                  0
## 30                     4                   5                  0
## 31                     2                   2                  0
## 32                     5                   8                  0
## 33                     2                   3                  0
## 34                     5                   5                  0
## 35                     1                   1                  0
## 36                     1                   3                  0
## 37                     2                   4                  0
## 38                     5                   8                  0
## 39                     9                   5                  0
## 40                     5                   5                  0
## 41                     7                   6                  0
## 42                     4                   4                  0
## 43                    10                   2                  0
## 44                    21                   2                  0
## 45                    42                   2                  0
## 46                     0                   5                  0
## 47                     1                   1                  1
## 48                     1                   6                  0
## 49                    11                   4                  0
## 50                    17                   4                  0
##    Calophyllum.longifolium Casearia.aculeata Casearia.arborea
## 1                        0                 0                1
## 2                        2                 0                1
## 3                        0                 0                3
## 4                        2                 0                2
## 5                        1                 0                4
## 6                        2                 0                1
## 7                        2                 0                2
## 8                        2                 1                3
## 9                        2                 0                9
## 10                       0                 0                7
## 11                       0                 0                2
## 12                       0                 0                1
## 13                       0                 1                0
## 14                       4                 0                4
## 15                       0                 0                6
## 16                       1                 0                1
## 17                       0                 1                0
## 18                       4                 0                0
## 19                       1                 0                4
## 20                       2                 0                6
## 21                       2                 1                0
## 22                       1                 1                0
## 23                       1                 0                1
## 24                       2                 0                1
## 25                       1                 1                3
## 26                       0                 0                1
## 27                       1                 2                0
## 28                       1                 0                2
## 29                       1                 0                0
## 30                       0                 1                0
## 31                       4                 0                1
## 32                       0                 1                0
## 33                       0                 0                0
## 34                       0                 7                8
## 35                       1                 0                3
## 36                       0                 1                5
## 37                       1                 1                1
## 38                       1                 0                2
## 39                       0                 0                2
## 40                       1                 1                4
## 41                       0                 1                1
## 42                       1                 1                1
## 43                       0                 0                0
## 44                       2                 1                1
## 45                       3                 0                0
## 46                       2                 0                2
## 47                       0                 0                1
## 48                       2                 0                2
## 49                       2                 0                0
## 50                       0                 0                1
##    Casearia.commersoniana Casearia.guianensis Casearia.sylvestris
## 1                       0                   0                   2
## 2                       0                   0                   1
## 3                       1                   0                   0
## 4                       0                   0                   0
## 5                       1                   0                   0
## 6                       0                   0                   3
## 7                       0                   0                   1
## 8                       0                   0                   0
## 9                       1                   0                   1
## 10                      0                   0                   1
## 11                      0                   0                   0
## 12                      0                   0                   1
## 13                      0                   0                   1
## 14                      0                   0                   0
## 15                      0                   0                   0
## 16                      0                   0                   2
## 17                      0                   1                   0
## 18                      0                   0                   1
## 19                      0                   0                   1
## 20                      0                   0                   1
## 21                      0                   0                   0
## 22                      0                   0                   2
## 23                      0                   0                   1
## 24                      0                   0                   2
## 25                      0                   0                   1
## 26                      0                   0                   1
## 27                      0                   0                   1
## 28                      0                   0                   0
## 29                      0                   0                   0
## 30                      0                   0                   5
## 31                      0                   0                   0
## 32                      0                   0                   4
## 33                      0                   0                   0
## 34                      0                   0                   1
## 35                      0                   0                   3
## 36                      0                   0                   2
## 37                      0                   0                   1
## 38                      0                   0                   0
## 39                      0                   0                   3
## 40                      0                   0                   2
## 41                      0                   0                   2
## 42                      0                   0                   2
## 43                      0                   0                   0
## 44                      0                   0                   1
## 45                      0                   0                   0
## 46                      0                   1                   3
## 47                      0                   0                   0
## 48                      0                   0                   0
## 49                      0                   0                   1
## 50                      0                   0                   0
##    Cassipourea.guianensis Cavanillesia.platanifolia Cecropia.insignis
## 1                       2                         0                12
## 2                       0                         0                 5
## 3                       1                         0                 7
## 4                       1                         0                17
## 5                       3                         0                21
## 6                       4                         0                 4
## 7                       4                         0                 0
## 8                       0                         0                 7
## 9                       2                         0                 2
## 10                      1                         0                16
## 11                      0                         0                 3
## 12                      2                         0                 2
## 13                      9                         0                 1
## 14                      3                         0                11
## 15                      0                         0                24
## 16                      1                         0                 2
## 17                      0                         0                 3
## 18                      6                         0                 0
## 19                      2                         0                 8
## 20                      3                         0                11
## 21                      1                         0                 2
## 22                      2                         0                 1
## 23                      6                         0                 2
## 24                      1                         0                 3
## 25                      2                         1                10
## 26                      2                         3                 1
## 27                      0                         1                 3
## 28                      3                         1                 3
## 29                      3                         0                 5
## 30                      3                         1                14
## 31                      0                         1                 3
## 32                      1                         1                 4
## 33                      0                         1                 6
## 34                      1                         1                 2
## 35                      0                         1                 2
## 36                      0                         0                 6
## 37                      2                         0                10
## 38                      2                         1                 6
## 39                      0                         1                 4
## 40                      0                         1                 2
## 41                      2                         0                 7
## 42                      2                         0                 2
## 43                      2                         1                 2
## 44                      0                         0                 0
## 45                      3                         0                 5
## 46                      1                         0                 1
## 47                      2                         2                 2
## 48                      0                         1                 0
## 49                      0                         0                 0
## 50                      2                         0                 0
##    Cecropia.obtusifolia Cedrela.odorata Ceiba.pentandra Celtis.schippii
## 1                     0               0               0               0
## 2                     0               0               1               0
## 3                     0               0               1               0
## 4                     0               0               0               2
## 5                     1               0               1               2
## 6                     0               0               0               0
## 7                     0               0               0               1
## 8                     2               0               1               0
## 9                     0               0               0               0
## 10                    2               0               1               0
## 11                    0               0               2               0
## 12                    1               0               0               1
## 13                    1               0               2               0
## 14                    1               0               0               0
## 15                    0               1               2               1
## 16                    0               0               1               2
## 17                    0               0               2               1
## 18                    0               0               0               0
## 19                    3               0               0               1
## 20                    0               0               1               3
## 21                    4               0               2               2
## 22                    0               0               2               1
## 23                    3               0               2               1
## 24                    0               0               1               4
## 25                    1               0               1               0
## 26                    0               0               1               0
## 27                    0               0               2               0
## 28                    0               0               0               0
## 29                    1               0               3               0
## 30                    1               0               1               1
## 31                    0               1               0               0
## 32                    0               0               1               1
## 33                    1               0               1               1
## 34                    1               0               0               1
## 35                    0               0               1               0
## 36                    0               0               1               0
## 37                    0               0               1               0
## 38                    0               0               1               1
## 39                    0               0               0               1
## 40                    0               0               0               0
## 41                    0               0               1               1
## 42                    0               0               0               0
## 43                    0               0               0               1
## 44                    1               0               0               1
## 45                    0               0               0               3
## 46                    0               0               2               0
## 47                    0               0               0               2
## 48                    0               0               0               1
## 49                    1               0               0               1
## 50                    0               0               0               0
##    Cespedesia.spathulata Chamguava.schippii Chimarrhis.parviflora
## 1                      0                  0                     0
## 2                      0                  0                     0
## 3                      0                  0                     0
## 4                      0                  0                     0
## 5                      0                  0                     0
## 6                      0                  0                     0
## 7                      0                  0                     0
## 8                      0                  0                     0
## 9                      0                  0                     0
## 10                     0                  0                     0
## 11                     0                  0                     0
## 12                     0                  0                     0
## 13                     0                  0                     1
## 14                     0                  0                     0
## 15                     0                  0                     0
## 16                     1                  0                     0
## 17                     0                  0                     0
## 18                     0                  2                     0
## 19                     0                  0                     0
## 20                     0                  0                     0
## 21                     0                  0                     0
## 22                     0                  0                     0
## 23                     0                  0                     0
## 24                     0                  1                     0
## 25                     0                  0                     0
## 26                     0                  0                     0
## 27                     0                  0                     0
## 28                     0                  0                     0
## 29                     0                  0                     0
## 30                     0                  0                     0
## 31                     0                  0                     0
## 32                     0                  0                     0
## 33                     0                  0                     0
## 34                     0                  0                     0
## 35                     0                  0                     0
## 36                     0                  0                     0
## 37                     0                  0                     0
## 38                     0                  0                     0
## 39                     0                  0                     0
## 40                     0                  0                     0
## 41                     0                  0                     0
## 42                     0                  0                     0
## 43                     0                  0                     0
## 44                     0                  0                     0
## 45                     0                  0                     0
## 46                     0                  0                     0
## 47                     0                  0                     0
## 48                     0                  0                     0
## 49                     1                  0                     0
## 50                     0                  0                     0
##    Maclura.tinctoria Chrysochlamys.eclipes Chrysophyllum.argenteum
## 1                  0                     0                       4
## 2                  0                     0                       1
## 3                  0                     0                       2
## 4                  0                     0                       2
## 5                  0                     0                       6
## 6                  0                     0                       2
## 7                  0                     0                       3
## 8                  0                     0                       2
## 9                  0                     0                       4
## 10                 0                     0                       2
## 11                 0                     0                       2
## 12                 0                     0                       1
## 13                 0                     0                       4
## 14                 0                     0                       2
## 15                 0                     0                       1
## 16                 0                     1                       2
## 17                 0                     0                       1
## 18                 1                     0                       0
## 19                 0                     0                       0
## 20                 0                     0                       2
## 21                 0                     0                       2
## 22                 0                     0                       0
## 23                 0                     0                       1
## 24                 0                     0                       2
## 25                 0                     0                       1
## 26                 0                     0                       0
## 27                 0                     0                       1
## 28                 0                     0                       0
## 29                 0                     0                       3
## 30                 0                     0                       1
## 31                 0                     0                       0
## 32                 0                     0                       1
## 33                 0                     0                       2
## 34                 0                     0                       1
## 35                 0                     0                       1
## 36                 0                     0                       3
## 37                 0                     0                       2
## 38                 0                     0                       0
## 39                 0                     0                       2
## 40                 0                     0                       0
## 41                 0                     1                       3
## 42                 0                     0                       2
## 43                 0                     0                       0
## 44                 0                     0                       1
## 45                 0                     0                       2
## 46                 0                     0                       1
## 47                 0                     0                       5
## 48                 0                     0                       1
## 49                 0                     0                       2
## 50                 0                     0                       2
##    Chrysophyllum.cainito Coccoloba.coronata Coccoloba.manzinellensis
## 1                      0                  0                        0
## 2                      0                  0                        0
## 3                      0                  0                        0
## 4                      0                  1                        0
## 5                      0                  2                        0
## 6                      0                  0                        0
## 7                      1                  0                        0
## 8                      0                  1                        2
## 9                      0                  2                        0
## 10                     0                  1                        0
## 11                     0                  0                        0
## 12                     0                  0                        0
## 13                     0                  1                        1
## 14                     2                  0                        0
## 15                     1                  1                        0
## 16                     0                  1                        0
## 17                     0                  0                        0
## 18                     2                  0                        2
## 19                     1                  0                        0
## 20                     0                  2                        0
## 21                     0                  1                        0
## 22                     1                  1                        1
## 23                     2                  1                        0
## 24                     1                  0                        0
## 25                     2                  1                        0
## 26                     0                  0                        0
## 27                     1                  0                        0
## 28                     0                  1                        0
## 29                     1                  0                        0
## 30                     0                  0                        2
## 31                     0                  1                        0
## 32                     0                  0                        0
## 33                     1                  2                        0
## 34                     2                  0                        1
## 35                     0                  0                        1
## 36                     0                  1                        1
## 37                     0                  0                        0
## 38                     0                  0                        0
## 39                     0                  0                        0
## 40                     1                  0                        0
## 41                     0                  0                        1
## 42                     0                  0                        0
## 43                     2                  0                        0
## 44                     0                  0                        0
## 45                     1                  0                        0
## 46                     1                  0                        0
## 47                     1                  0                        1
## 48                     0                  0                        0
## 49                     0                  1                        0
## 50                     1                  0                        0
##    Colubrina.glandulosa Cordia.alliodora Cordia.bicolor Cordia.lasiocalyx
## 1                     0                2             12                 8
## 2                     0                3             14                 6
## 3                     0                3             35                 6
## 4                     0                7             23                11
## 5                     0                1             13                 7
## 6                     0                1              7                 6
## 7                     0                2              5                 6
## 8                     0                0             10                 3
## 9                     0                0              7                 0
## 10                    0                2             13                 4
## 11                    0                3             10                 5
## 12                    0                0              2                 3
## 13                    0                2              0                 4
## 14                    0                1             11                 7
## 15                    0                1             21                 3
## 16                    0                1             11                10
## 17                    0                0              7                 3
## 18                    0                2              2                 3
## 19                    0                5              8                 4
## 20                    0                0             17                 4
## 21                    0                0              5                11
## 22                    1                0              4                 5
## 23                    0                0              2                10
## 24                    0                0              3                 4
## 25                    0                0              3                 4
## 26                    0                1              1                 8
## 27                    0                0              3                 9
## 28                    0                0              4                 4
## 29                    0                2              3                 5
## 30                    0                2              5                 0
## 31                    0                2              0                 6
## 32                    0                0              3                 7
## 33                    0                0              3                11
## 34                    0                2              0                 5
## 35                    0                0              3                 4
## 36                    0                0              9                10
## 37                    0                6              2                13
## 38                    0                2              3                 8
## 39                    0                0              1                 8
## 40                    0                0              2                 3
## 41                    0                1              6                12
## 42                    0                0              9                12
## 43                    0                1              2                12
## 44                    0                0              3                20
## 45                    0                0              1                 8
## 46                    0                6              7                17
## 47                    0                1              3                13
## 48                    0                0              3                14
## 49                    0                0              2                 7
## 50                    0                1              2                11
##    Coussarea.curvigemma Croton.billbergianus Cupania.cinerea Cupania.latifolia
## 1                     0                    2               0                 0
## 2                     0                    2               0                 0
## 3                     0                    0               0                 0
## 4                     1                   11               0                 1
## 5                     0                    6               0                 0
## 6                     2                    0               0                 0
## 7                     1                    0               0                 0
## 8                     0                    4               0                 0
## 9                     1                    2               0                 0
## 10                    1                    0               0                 0
## 11                    0                    1               0                 0
## 12                    3                    2               0                 0
## 13                    4                   12               0                 0
## 14                    0                   11               0                 0
## 15                    0                    1               0                 0
## 16                    1                    3               0                 2
## 17                    4                    0               0                 0
## 18                    6                    4               0                 0
## 19                    3                    1               1                 0
## 20                    0                    0               0                 1
## 21                    0                    1               0                 0
## 22                   11                    0               0                 0
## 23                    2                    2               0                 0
## 24                    1                    0               0                 0
## 25                    0                    1               0                 0
## 26                    0                    1               0                 0
## 27                    2                    0               0                 1
## 28                    2                    0               0                 0
## 29                    0                    1               0                 0
## 30                    2                    2               0                 0
## 31                    0                    0               0                 0
## 32                    0                    0               0                 0
## 33                    0                    0               0                 0
## 34                    0                    0               0                 1
## 35                    1                    1               0                 0
## 36                    0                    0               0                 1
## 37                    0                    2               0                 1
## 38                    0                    2               0                 0
## 39                    0                    0               0                 0
## 40                    0                    1               0                 0
## 41                    0                    6               0                 3
## 42                    0                    3               0                 0
## 43                    0                    0               0                 0
## 44                    0                    0               0                 0
## 45                    0                    1               0                 0
## 46                    5                    0               0                 1
## 47                    1                    3               0                 0
## 48                    1                    6               0                 0
## 49                    0                    2               0                 0
## 50                    0                    1               0                 0
##    Cupania.rufescens Cupania.seemannii Dendropanax.arboreus
## 1                  0                 2                    0
## 2                  0                 2                    3
## 3                  0                 1                    6
## 4                  0                 0                    0
## 5                  0                 3                    5
## 6                  0                 0                    2
## 7                  0                 1                    1
## 8                  0                 2                    6
## 9                  0                 2                    1
## 10                 0                 0                    3
## 11                 0                 2                    2
## 12                 0                 1                    2
## 13                 1                 2                    5
## 14                 0                 0                    2
## 15                 0                 4                    5
## 16                 0                 0                    3
## 17                 2                 3                    2
## 18                 1                 0                    2
## 19                 0                 1                    3
## 20                 0                 2                    1
## 21                 0                 2                    3
## 22                 0                 0                    0
## 23                 0                 1                    1
## 24                 0                 1                    3
## 25                 0                 1                   10
## 26                 0                 0                    0
## 27                 0                 2                    0
## 28                 0                 0                    0
## 29                 0                 2                    2
## 30                 0                 1                    3
## 31                 0                 0                    0
## 32                 0                 1                    0
## 33                 0                 0                    1
## 34                 0                 0                    2
## 35                 0                 1                    0
## 36                 0                 1                    0
## 37                 0                 0                    1
## 38                 0                 0                    1
## 39                 0                 1                    0
## 40                 0                 0                    1
## 41                 0                 1                    1
## 42                 0                 1                    0
## 43                 0                 0                    1
## 44                 0                 0                    0
## 45                 0                 0                    2
## 46                 0                 1                    0
## 47                 0                 1                    0
## 48                 0                 0                    0
## 49                 0                 0                    1
## 50                 0                 1                    1
##    Desmopsis.panamensis Diospyros.artanthifolia Dipteryx.oleifera
## 1                     0                       1                 1
## 2                     0                       1                 1
## 3                     4                       1                 3
## 4                     0                       1                 0
## 5                     0                       0                 0
## 6                     0                       0                 0
## 7                     0                       0                 0
## 8                     0                       0                 2
## 9                     0                       0                 1
## 10                    1                       1                 2
## 11                    0                       1                 0
## 12                    0                       0                 0
## 13                    0                       0                 0
## 14                    0                       0                 1
## 15                    0                       0                 1
## 16                    0                       0                 0
## 17                    0                       1                 0
## 18                    0                       0                 0
## 19                    1                       0                 1
## 20                    0                       0                 2
## 21                    0                       0                 0
## 22                    0                       2                 0
## 23                    1                       0                 0
## 24                    0                       0                 0
## 25                    0                       0                 0
## 26                    0                       0                 1
## 27                    0                       0                 1
## 28                    0                       0                 3
## 29                    0                       0                 1
## 30                    0                       0                 2
## 31                    0                       1                 0
## 32                    0                       0                 1
## 33                    1                       0                 1
## 34                    1                       0                 0
## 35                    0                       0                 0
## 36                    1                       0                 1
## 37                    1                       0                 0
## 38                    0                       1                 0
## 39                    1                       0                 0
## 40                    0                       0                 0
## 41                    0                       0                 0
## 42                    0                       0                 0
## 43                    0                       0                 2
## 44                    1                       0                 1
## 45                    0                       0                 2
## 46                    0                       3                 1
## 47                    0                       2                 0
## 48                    0                       0                 0
## 49                    0                       0                 0
## 50                    0                       0                 1
##    Drypetes.standleyi Elaeis.oleifera Enterolobium.schomburgkii
## 1                   2               0                         0
## 2                   1               0                         0
## 3                   2               0                         0
## 4                   0               0                         0
## 5                   0               0                         0
## 6                   0               0                         0
## 7                   0               0                         0
## 8                   0               0                         0
## 9                   0               0                         0
## 10                  0               0                         0
## 11                  3               0                         0
## 12                  2               0                         0
## 13                  0               6                         0
## 14                  0               0                         0
## 15                  0               0                         0
## 16                  2               0                         0
## 17                  3               0                         0
## 18                  1               9                         0
## 19                  1               1                         1
## 20                  0               0                         0
## 21                  7               0                         0
## 22                  4               0                         0
## 23                  0               5                         0
## 24                  0               0                         0
## 25                  2               0                         0
## 26                  8               0                         0
## 27                  7               0                         0
## 28                  2               0                         0
## 29                  4               0                         0
## 30                  3               0                         1
## 31                 15               0                         0
## 32                  6               0                         0
## 33                  2               0                         0
## 34                  1               0                         0
## 35                  1               0                         0
## 36                 39               0                         0
## 37                 13               0                         0
## 38                 12               0                         0
## 39                  2               0                         0
## 40                  0               0                         0
## 41                 21               0                         0
## 42                 14               0                         0
## 43                 17               0                         0
## 44                  8               0                         0
## 45                  7               0                         0
## 46                 33               0                         0
## 47                 12               0                         0
## 48                 11               0                         0
## 49                  5               0                         0
## 50                 12               0                         0
##    Erythrina.costaricensis Erythroxylum.macrophyllum Eugenia.florida
## 1                        0                         0               0
## 2                        0                         1               1
## 3                        0                         0               0
## 4                        0                         0               7
## 5                        0                         0               2
## 6                        3                         0               0
## 7                        0                         0               0
## 8                        0                         1               1
## 9                        1                         1               1
## 10                       0                         1               3
## 11                       1                         0               1
## 12                       0                         1               1
## 13                       0                         0               2
## 14                       1                         0               1
## 15                       1                         1               0
## 16                       1                         0               0
## 17                       0                         0               2
## 18                       0                         0               2
## 19                       0                         0               2
## 20                       1                         1               1
## 21                       0                         0               1
## 22                       0                         2               1
## 23                       1                         1               2
## 24                       3                         0               1
## 25                       0                         1               2
## 26                       1                         0               1
## 27                       0                         1               1
## 28                       0                         0               0
## 29                       0                         0               5
## 30                       0                         1               3
## 31                       0                         0               0
## 32                       0                         0               1
## 33                       0                         0               1
## 34                       0                         0               4
## 35                       0                         1               1
## 36                       1                         0               2
## 37                       1                         1               2
## 38                       0                         0               3
## 39                       0                         0               4
## 40                       0                         0               1
## 41                       0                         0               1
## 42                       1                         0               2
## 43                       2                         0               3
## 44                       4                         0               2
## 45                       1                         0               1
## 46                       0                         0               4
## 47                       0                         0               4
## 48                       0                         1               1
## 49                       2                         1               0
## 50                       0                         1               0
##    Eugenia.galalonensis Eugenia.nesiotica Eugenia.oerstediana
## 1                     0                 0                   3
## 2                     0                 0                   2
## 3                     0                 1                   5
## 4                     0                 0                   1
## 5                     0                 0                   5
## 6                     0                 0                   2
## 7                     0                 5                   2
## 8                     1                 4                   3
## 9                     0                 3                   3
## 10                    0                 0                   3
## 11                    0                 0                   6
## 12                    1                 2                   1
## 13                    0                 2                  11
## 14                    0                 3                   1
## 15                    0                 2                   4
## 16                    0                 0                   7
## 17                    0                 2                   3
## 18                    0                 2                   4
## 19                    1                 1                   6
## 20                    0                 0                   2
## 21                    1                 1                   2
## 22                    0                 1                   2
## 23                    0                 1                   2
## 24                    0                 0                   2
## 25                    1                 0                   6
## 26                    1                 0                   1
## 27                    0                 2                   3
## 28                    0                 1                   5
## 29                    1                 0                   1
## 30                    0                 0                   5
## 31                    0                 0                   3
## 32                    0                 1                   2
## 33                    0                 1                   5
## 34                    0                 3                   7
## 35                    0                 0                   6
## 36                    0                 2                   0
## 37                    0                 0                   4
## 38                    0                 1                  10
## 39                    0                 2                   4
## 40                    2                 2                   3
## 41                    0                 0                   7
## 42                    0                 0                   8
## 43                    0                 3                   4
## 44                    0                 0                   3
## 45                    0                 1                   2
## 46                    0                 1                   0
## 47                    1                 1                   2
## 48                    0                 1                   1
## 49                    0                 2                   1
## 50                    2                 1                   2
##    Faramea.occidentalis Ficus.colubrinae Ficus.costaricana Ficus.insipida
## 1                    14                0                 0              0
## 2                    36                1                 0              0
## 3                    39                0                 0              0
## 4                    39                0                 0              0
## 5                    22                0                 0              0
## 6                    16                0                 0              0
## 7                    38                0                 0              0
## 8                    41                0                 0              0
## 9                    33                0                 0              0
## 10                   42                0                 0              0
## 11                   17                0                 0              0
## 12                   38                0                 0              0
## 13                   39                0                 0              1
## 14                   31                0                 0              0
## 15                   31                0                 0              0
## 16                   27                0                 0              0
## 17                   42                0                 0              0
## 18                   35                0                 1              0
## 19                   42                0                 0              0
## 20                   21                0                 1              0
## 21                   17                0                 0              0
## 22                   58                0                 0              0
## 23                   26                0                 1              1
## 24                   24                0                 0              0
## 25                   35                0                 0              0
## 26                   31                0                 0              0
## 27                   51                0                 0              0
## 28                   58                0                 0              0
## 29                   54                0                 0              0
## 30                   61                0                 0              0
## 31                   30                0                 0              0
## 32                   60                0                 0              0
## 33                   53                0                 0              0
## 34                   49                0                 0              0
## 35                   37                0                 0              0
## 36                   32                0                 1              0
## 37                   65                0                 0              0
## 38                   80                0                 1              0
## 39                   43                0                 2              0
## 40                   41                0                 0              1
## 41                   22                0                 0              0
## 42                   25                0                 0              0
## 43                   15                0                 0              0
## 44                   15                0                 0              0
## 45                   10                0                 0              0
## 46                   22                0                 0              0
## 47                   27                0                 0              0
## 48                   15                0                 0              0
## 49                   11                0                 0              0
## 50                    7                0                 0              0
##    Ficus.maxima Ficus.obtusifolia Ficus.popenoei Ficus.tonduzii Ficus.trigonata
## 1             1                 0              0              0               0
## 2             0                 0              0              0               0
## 3             0                 0              0              1               0
## 4             0                 0              0              2               0
## 5             0                 0              0              1               0
## 6             0                 0              0              0               0
## 7             0                 0              1              0               0
## 8             0                 0              0              0               0
## 9             0                 0              0              0               0
## 10            0                 0              0              0               0
## 11            0                 0              0              0               0
## 12            0                 0              1              1               0
## 13            0                 0              0              0               0
## 14            0                 1              0              0               0
## 15            0                 0              0              2               0
## 16            0                 0              0              1               0
## 17            0                 0              0              0               0
## 18            0                 0              0              0               0
## 19            0                 0              0              0               0
## 20            0                 0              0              3               0
## 21            0                 0              0              0               0
## 22            1                 1              0              0               0
## 23            0                 0              0              0               0
## 24            0                 2              0              0               0
## 25            0                 0              0              1               0
## 26            0                 0              0              0               0
## 27            0                 0              0              0               0
## 28            0                 0              0              0               0
## 29            0                 0              0              0               0
## 30            0                 0              0              0               0
## 31            1                 0              0              1               0
## 32            0                 0              0              0               0
## 33            0                 1              0              0               0
## 34            0                 0              0              0               1
## 35            0                 0              0              0               0
## 36            0                 0              0              1               0
## 37            0                 0              0              1               0
## 38            0                 0              0              1               0
## 39            0                 0              0              0               0
## 40            0                 0              0              0               0
## 41            1                 1              0              0               0
## 42            0                 0              0              2               1
## 43            0                 0              0              2               1
## 44            0                 0              1              0               1
## 45            0                 0              0              0               0
## 46            0                 0              0              0               0
## 47            0                 1              0              0               0
## 48            0                 0              0              1               0
## 49            0                 0              0              1               0
## 50            0                 0              0              1               1
##    Ficus.yoponensis Garcinia.intermedia Garcinia.madruno Genipa.americana
## 1                 1                   0                4                0
## 2                 0                   1                0                0
## 3                 0                   1                0                1
## 4                 0                   3                0                0
## 5                 0                   2                1                0
## 6                 1                   1                0                0
## 7                 1                   2                0                1
## 8                 0                   2                0                0
## 9                 0                   1                0                1
## 10                0                   0                1                1
## 11                0                   1                0                0
## 12                0                   3                0                0
## 13                0                   3                0                1
## 14                0                   1                0                1
## 15                0                   0                1                0
## 16                0                   1                0                2
## 17                0                   0                0                1
## 18                0                   2                0                1
## 19                0                   3                0                0
## 20                0                   0                1                0
## 21                0                   1                0                0
## 22                0                   3                0                0
## 23                0                   2                1                0
## 24                0                   1                0                0
## 25                1                   3                1                0
## 26                0                   2                0                1
## 27                0                   2                1                0
## 28                0                   4                0                0
## 29                0                   1                0                1
## 30                0                   1                0                0
## 31                0                   0                0                0
## 32                0                   3                0                0
## 33                0                   0                0                0
## 34                0                   4                1                0
## 35                1                   2                0                0
## 36                0                   0                0                1
## 37                0                   1                0                0
## 38                0                   2                0                0
## 39                0                   6                0                1
## 40                0                   6                0                0
## 41                0                   0                0                2
## 42                0                   0                0                0
## 43                0                   2                0                0
## 44                0                   4                0                0
## 45                0                   0                0                1
## 46                0                   8                0                1
## 47                1                   3                0                1
## 48                0                   0                0                0
## 49                0                   0                0                1
## 50                0                   4                0                3
##    Guapira.myrtiflora Guarea.fuzzy Guarea.grandifolia Guarea.guidonia
## 1                   3            1                  0               2
## 2                   1            1                  0               6
## 3                   0            0                  0               2
## 4                   1            1                  0               5
## 5                   1            3                  0               3
## 6                   7            0                  0               4
## 7                   3            0                  0               4
## 8                   1            2                  1               0
## 9                   1            0                  0               1
## 10                  1            3                  0               5
## 11                  1            1                  1               5
## 12                  3            1                  0               3
## 13                  2            0                  0               4
## 14                  0            0                  0               3
## 15                  1            2                  2               0
## 16                  2            2                  0               7
## 17                  1            0                  0               2
## 18                  0            0                  0               2
## 19                  3            0                  0               2
## 20                  1            1                  1               5
## 21                  3            3                  0               7
## 22                  3            0                  1               4
## 23                  1            2                  0               6
## 24                  7            0                  0               8
## 25                  2            1                  0               6
## 26                  2            1                  0               6
## 27                  4            1                  0              12
## 28                  2            2                  0               8
## 29                  2            3                  1               3
## 30                  2            2                  0               2
## 31                  2            0                  0               9
## 32                  0            2                  0              11
## 33                  4            1                  1              27
## 34                  2            5                  0              16
## 35                  1            0                  0               3
## 36                  2            2                  0              10
## 37                  1            2                  1              24
## 38                  5            2                  0              12
## 39                  3            1                  1               9
## 40                  4            2                  0               6
## 41                  1            0                  0              18
## 42                  1            1                  0               8
## 43                  1            1                  0              16
## 44                  0            3                  0               8
## 45                  2            7                  0              11
## 46                  2            2                  0               4
## 47                  2            0                  0              10
## 48                  4            1                  0              13
## 49                  1            1                  0              20
## 50                  0            2                  0              14
##    Guatteria.dumetorum Guazuma.ulmifolia Guettarda.foliacea Gustavia.superba
## 1                    6                 0                  1               10
## 2                   16                 0                  5                5
## 3                    6                 0                  1                0
## 4                    3                 1                  2                1
## 5                    9                 0                  1                3
## 6                    7                 0                  0                1
## 7                    8                 0                  0                8
## 8                    6                 0                  4                4
## 9                    2                 0                  1                4
## 10                   2                 0                  3                4
## 11                   3                 0                  1                2
## 12                   2                 0                  0                3
## 13                   0                 2                  2               10
## 14                   7                 1                  0                4
## 15                  16                 1                  4                4
## 16                   5                 1                  0               10
## 17                   3                 0                  1                7
## 18                   0                 1                  2                3
## 19                   3                 1                  1                6
## 20                   7                 2                  4                4
## 21                  10                 0                  0                6
## 22                   5                 0                  0                9
## 23                   2                 1                  0                3
## 24                   5                 1                  3                4
## 25                   2                 2                  3               14
## 26                  13                 0                  0                8
## 27                   3                 2                  0                3
## 28                   3                 1                  1                8
## 29                   5                 1                  0                6
## 30                   1                 2                  6               23
## 31                  10                 0                  1                2
## 32                  11                 0                  2                8
## 33                   3                 0                  0                6
## 34                   1                 5                  3               25
## 35                   0                 5                  7              247
## 36                   8                 2                  2                1
## 37                   5                 0                  0                1
## 38                   3                 0                  2               11
## 39                   1                 2                  2               22
## 40                   4                 0                  3               63
## 41                   5                 1                  1                6
## 42                   7                 0                  2                4
## 43                   5                 1                  1                1
## 44                   6                 0                  2               17
## 45                   1                 0                  0                2
## 46                   1                 0                  1               11
## 47                   0                 0                  4               11
## 48                   2                 1                  3                4
## 49                   7                 1                  1               15
## 50                   4                 0                  2               10
##    Hampea.appendiculata Hasseltia.floribunda Heisteria.acuminata
## 1                     0                    5                   0
## 2                     0                    9                   0
## 3                     1                    4                   0
## 4                     0                   11                   0
## 5                     0                    9                   1
## 6                     0                    2                   1
## 7                     0                    7                   0
## 8                     0                    6                   0
## 9                     2                    3                   0
## 10                    1                    4                   0
## 11                    0                    5                   0
## 12                    1                    0                   0
## 13                    0                    1                   0
## 14                    0                    4                   1
## 15                    0                   20                   0
## 16                    0                    7                   0
## 17                    0                    1                   0
## 18                    0                    2                   0
## 19                    0                    3                   0
## 20                    0                    6                   0
## 21                    0                    3                   1
## 22                    0                    5                   0
## 23                    0                    6                   0
## 24                    1                    5                   0
## 25                    1                    3                   0
## 26                    0                    7                   1
## 27                    0                    1                   0
## 28                    0                    3                   0
## 29                    1                    1                   0
## 30                    0                   10                   0
## 31                    0                    2                   0
## 32                    0                    7                   0
## 33                    0                    4                   0
## 34                    0                    1                   0
## 35                    0                    7                   0
## 36                    1                    1                   1
## 37                    1                    3                   0
## 38                    0                    2                   0
## 39                    0                    2                   0
## 40                    1                    3                   0
## 41                    0                    1                   1
## 42                    1                    4                   0
## 43                    0                    6                   0
## 44                    0                    6                   0
## 45                    1                    1                   0
## 46                    0                    0                   0
## 47                    0                    1                   0
## 48                    0                    2                   0
## 49                    0                    7                   0
## 50                    0                   16                   0
##    Heisteria.concinna Hirtella.americana Hirtella.triandra Hura.crepitans
## 1                   4                  0                21              0
## 2                   5                  0                14              0
## 3                   4                  0                 5              0
## 4                   6                  0                 4              0
## 5                   4                  0                 6              0
## 6                   8                  0                 6              2
## 7                   2                  0                 7              1
## 8                   5                  0                14              1
## 9                   1                  0                 8              0
## 10                  5                  0                 7              0
## 11                  5                  0                12              0
## 12                 12                  0                 6              2
## 13                  4                  0                11              1
## 14                  0                  0                13              0
## 15                  3                  0                 4              0
## 16                  2                  0                 4              3
## 17                 13                  0                 4              0
## 18                  8                  0                12              0
## 19                  7                  0                24              0
## 20                  1                  0                12              0
## 21                  1                  0                17              0
## 22                  9                  0                 6              2
## 23                  5                  0                10              5
## 24                  7                  1                15              0
## 25                  3                  0                26              0
## 26                  4                  0                24              4
## 27                  1                  0                 8              2
## 28                  4                  0                 9              2
## 29                  5                  0                 7              5
## 30                  0                  0                 3              1
## 31                  6                  0                14              3
## 32                  6                  0                 8              7
## 33                  5                  0                 9              2
## 34                  4                  0                 4              5
## 35                  2                  0                 1              0
## 36                  4                  0                24              2
## 37                  6                  0                 7              3
## 38                 15                  0                 3              2
## 39                 12                  0                 3              2
## 40                  3                  0                 7              3
## 41                  6                  0                31              2
## 42                  4                  0                18              3
## 43                 10                  0                23              1
## 44                  6                  0                18              6
## 45                 18                  0                26              7
## 46                 15                  4                22              5
## 47                  6                  0                33              7
## 48                  3                  0                41              7
## 49                  8                  0                43              1
## 50                 11                  0                27              2
##    Hieronyma.alchorneoides Inga.acuminata Inga.cocleensis Inga.goldmanii
## 1                        0              0               2              0
## 2                        2              0               4              0
## 3                        0              0               4              1
## 4                        0              0               6              0
## 5                        0              0               0              2
## 6                        0              0               0              1
## 7                        0              0               1              0
## 8                        0              0               6              1
## 9                        1              0               4              1
## 10                       0              0               5              2
## 11                       0              0               0              1
## 12                       0              0               0              0
## 13                       1              0               2              1
## 14                       2              0               3              1
## 15                       0              0               2              2
## 16                       0              7               0              0
## 17                       0              2               2              1
## 18                       2              0               1              2
## 19                       1              0               2              0
## 20                       3              0               2              3
## 21                       1              0               0              0
## 22                       1              1               3              2
## 23                       5              0               1              6
## 24                       0              0               0              1
## 25                       2              0               0              0
## 26                       1              2               0              1
## 27                       0              0               0              2
## 28                       2              1               0              2
## 29                       1              0               0              0
## 30                       0              0               0              1
## 31                       1              0               0              0
## 32                       0              0               0              1
## 33                       0              0               0              2
## 34                       0              0               0              1
## 35                       3              0               0              0
## 36                       1              0               0              2
## 37                       3              3               0              2
## 38                       1              0               0              0
## 39                       0              0               0              0
## 40                       1              0               0              1
## 41                       2              1               0              1
## 42                       1              2               0              0
## 43                       0              3               0              0
## 44                       0              0               0              1
## 45                       0              0               0              0
## 46                       0              0               2              1
## 47                       2              3               0              1
## 48                       0              1               0              1
## 49                       1              0               0              1
## 50                       0              0               0              0
##    Inga.laurina Inga.semialata Inga.nobilis Inga.oerstediana Inga.pezizifera
## 1             0              0            0                0               0
## 2             0              0            0                0               0
## 3             0              2            1                0               0
## 4             0              4            3                0               0
## 5             1              0            1                0               0
## 6             0              0            0                0               0
## 7             0              0            2                0               0
## 8             0              4            2                0               0
## 9             0              1            2                0               0
## 10            0              1            3                0               0
## 11            0              2            0                0               0
## 12            1              1            0                0               0
## 13            1              0            0                0               0
## 14            0              1            0                0               0
## 15            0              8            5                0               0
## 16            0              6            0                0               0
## 17            0              0            1                0               0
## 18            0              1            1                0               0
## 19            1              0            0                0               0
## 20            0              9            2                0               0
## 21            1              1            1                1               0
## 22            0              2            0                0               0
## 23            0              0            0                0               0
## 24            0              2            1                0               0
## 25            0              1            0                0               0
## 26            0              2            2                0               0
## 27            0              1            2                0               0
## 28            0              2            1                0               0
## 29            0              1            0                1               0
## 30            1              1            1                0               0
## 31            0              1            0                0               0
## 32            0              1            2                0               0
## 33            0              0            0                0               0
## 34            0              0            2                0               0
## 35            0              1            0                0               0
## 36            0              3            0                0               0
## 37            0              2            0                0               0
## 38            0              3            1                0               0
## 39            0              4            1                0               0
## 40            0              7            1                0               3
## 41            0              3            2                0               0
## 42            0              7            3                0               0
## 43            0              0            6                0               2
## 44            0              1            2                0               5
## 45            0              3            2                0               3
## 46            3              1            2                0               0
## 47            1              1            3                0               3
## 48            0              4            3                0               0
## 49            0              3            2                0               1
## 50            0              0            4                0               3
##    Inga.punctata Inga.ruiziana Inga.sapindoides Inga.spectabilis
## 1              3             0                2                0
## 2              0             0                0                2
## 3              0             0                3                0
## 4              0             0                2                1
## 5              0             0                5                0
## 6              0             0                0                0
## 7              0             0                0                0
## 8              0             0                1                0
## 9              0             0                1                0
## 10             0             0                0                0
## 11             0             0                0                1
## 12             0             0                2                0
## 13             0             0                0                0
## 14             0             0                4                2
## 15             0             0                1                1
## 16             0             0                0                0
## 17             0             0                1                1
## 18             0             3                1                0
## 19             0             0                3                1
## 20             1             0                1                1
## 21             1             1                1                0
## 22             0             0                2                0
## 23             0             0                0                0
## 24             0             0                4                0
## 25             0             0                2                0
## 26             0             0                0                0
## 27             1             0                1                0
## 28             0             0                4                0
## 29             0             0                0                0
## 30             0             0                2                1
## 31             0             0                2                0
## 32             0             0                2                0
## 33             0             0                1                0
## 34             1             0                3                0
## 35             1             0                2                0
## 36             0             0                2                0
## 37             0             0                3                0
## 38             0             0                1                0
## 39             0             0                0                0
## 40             0             0                1                0
## 41             1             0                2                1
## 42             0             0                3                1
## 43             0             0                1                0
## 44             0             0                1                1
## 45             0             0                0                0
## 46             0             0                1                0
## 47             0             0                1                0
## 48             0             0                3                0
## 49             0             0                2                0
## 50             1             1                2                0
##    Inga.umbellifera Jacaranda.copaia Lacistema.aggregatum Lacmellea.panamensis
## 1                 0                6                    1                    1
## 2                 0               10                    0                    0
## 3                 0                9                    0                    0
## 4                 1                2                    1                    2
## 5                 0                3                    1                    2
## 6                 0                7                    2                    1
## 7                 0                4                    1                    3
## 8                 2                8                    0                    2
## 9                 2                5                    0                    0
## 10                1               12                    2                    0
## 11                0                7                    0                    0
## 12                0                2                    0                    1
## 13                0                3                    0                    1
## 14                0               12                    0                    2
## 15                1               23                    1                    1
## 16                0                6                    1                    0
## 17                0                4                    2                    1
## 18                0                3                    0                    3
## 19                1                7                    1                    4
## 20                0               10                    1                    1
## 21                0                8                    0                    1
## 22                0                6                    1                    0
## 23                0                4                    0                    2
## 24                0                2                    0                    0
## 25                0                5                    2                    1
## 26                0                0                    1                    0
## 27                0                3                    1                    1
## 28                0                3                    1                    0
## 29                0                3                    1                    1
## 30                0                3                    0                    2
## 31                1                0                    0                    0
## 32                0                3                    1                    0
## 33                1                6                    2                    1
## 34                0                2                    0                    1
## 35                1                3                    1                    1
## 36                1                3                    1                    1
## 37                0                2                    0                    0
## 38                0                1                    0                    3
## 39                0                1                    2                    1
## 40                0                1                    0                    1
## 41                0                3                    0                    1
## 42                0                3                    3                    1
## 43                0                2                    0                    1
## 44                1                0                    0                    0
## 45                0                1                    1                    0
## 46                0                7                    0                    2
## 47                1               13                    1                    2
## 48                0                1                    0                    2
## 49                0                3                    0                    0
## 50                0                1                    0                    0
##    Laetia.procera Laetia.thamnia Lafoensia.punicifolia Licania.hypoleuca
## 1               0              0                     0                 0
## 2               1              1                     0                 0
## 3               1              1                     0                 0
## 4               0              0                     0                 0
## 5               1              0                     0                 1
## 6               0              0                     0                 0
## 7               0              0                     0                 0
## 8               1              2                     0                 1
## 9               0              1                     0                 0
## 10              0              1                     0                 1
## 11              1              1                     0                 0
## 12              1              0                     0                 0
## 13              0              3                     0                 1
## 14              1              3                     1                 0
## 15              0              2                     0                 1
## 16              0              0                     0                 0
## 17              1              1                     0                 0
## 18              2              0                     0                 0
## 19              1              3                     4                 2
## 20              0              2                     0                 1
## 21              1              0                     0                 0
## 22              0              0                     0                 1
## 23              0              1                     0                 0
## 24              0              2                     0                 0
## 25              0              1                     0                 1
## 26              0              0                     0                 0
## 27              0              1                     0                 0
## 28              0              0                     0                 0
## 29              0              0                     0                 1
## 30              0              0                     0                 0
## 31              0              0                     0                 0
## 32              0              0                     0                 0
## 33              0              0                     0                 0
## 34              0              0                     0                 0
## 35              0              0                     0                 1
## 36              0              1                     0                 0
## 37              0              0                     0                 0
## 38              0              0                     0                 0
## 39              0              0                     0                 0
## 40              0              0                     0                 0
## 41              0              0                     0                 1
## 42              0              0                     0                 0
## 43              0              0                     0                 0
## 44              0              0                     0                 0
## 45              0              0                     0                 0
## 46              0              0                     0                 0
## 47              0              0                     0                 0
## 48              0              0                     0                 0
## 49              0              0                     0                 1
## 50              0              0                     0                 0
##    Licania.platypus Lindackeria.laurina Lonchocarpus.heptaphyllus
## 1                 0                   0                         7
## 2                 0                   0                         7
## 3                 0                   0                         3
## 4                 0                   0                         9
## 5                 0                   0                         2
## 6                 0                   0                         1
## 7                 1                   1                         4
## 8                 0                   0                         2
## 9                 0                   2                         2
## 10                0                   2                         4
## 11                1                   0                         2
## 12                0                   1                         3
## 13                0                   3                         4
## 14                0                   4                         3
## 15                0                   0                         2
## 16                0                   0                         2
## 17                0                   2                         5
## 18                0                   5                         3
## 19                0                   3                         1
## 20                0                   2                         1
## 21                1                   0                         2
## 22                0                   2                         1
## 23                1                   2                         4
## 24                0                   6                         2
## 25                0                   2                         2
## 26                0                   1                         2
## 27                0                   2                         0
## 28                0                   1                         0
## 29                0                   2                         3
## 30                0                   1                         7
## 31                0                   0                         3
## 32                0                   2                         1
## 33                0                   0                         1
## 34                0                   0                         1
## 35                0                   2                         2
## 36                0                   0                         4
## 37                0                   0                         2
## 38                0                   0                         0
## 39                0                   1                         1
## 40                0                   0                         3
## 41                1                   2                         1
## 42                0                   0                         1
## 43                0                   1                         2
## 44                0                   0                         0
## 45                0                   0                         1
## 46                0                   7                         2
## 47                1                   3                         3
## 48                2                   0                         1
## 49                2                   1                         0
## 50                0                   1                         2
##    Luehea.seemannii Macrocnemum.roseum Maquira.guianensis.costaricana
## 1                 1                  0                              4
## 2                 0                  0                              3
## 3                 0                  0                              7
## 4                 0                  0                              7
## 5                 1                  0                             10
## 6                 1                  0                              4
## 7                 2                  0                              3
## 8                 0                  0                              4
## 9                 1                  0                              7
## 10                0                  0                              3
## 11                4                  0                              6
## 12                1                  0                              3
## 13                4                  0                              2
## 14                1                  0                              0
## 15                0                  0                              4
## 16                4                  0                              4
## 17                1                  0                              2
## 18                5                  0                              0
## 19                4                  0                              1
## 20                0                  0                              2
## 21                4                  0                              5
## 22                2                  0                              2
## 23                6                  0                              2
## 24                0                  0                              5
## 25                2                  0                              4
## 26                1                  1                              7
## 27                3                  1                              3
## 28                3                  0                              2
## 29                1                  0                              2
## 30                5                  0                              2
## 31                2                  0                              4
## 32                3                  3                              3
## 33                4                  0                              3
## 34                3                  2                              3
## 35                6                  6                              1
## 36                2                  0                              5
## 37                2                  2                              0
## 38                2                  0                              3
## 39                2                  0                              1
## 40                1                  4                              0
## 41                2                  1                              2
## 42                2                  0                              4
## 43                1                  1                              4
## 44                1                  0                              5
## 45                0                  0                              7
## 46                0                  0                              0
## 47                1                  2                              1
## 48                1                  1                              4
## 49                1                  0                              5
## 50                0                  1                              2
##    Margaritaria.nobilis Marila.laxiflora Maytenus.schippii Miconia.affinis
## 1                     0                1                 2               0
## 2                     0                0                 0               0
## 3                     0                0                 0               0
## 4                     0                0                 1               1
## 5                     1                0                 0               0
## 6                     0                0                 1               0
## 7                     0                0                 2               0
## 8                     0                0                 0               1
## 9                     0                0                 0               0
## 10                    0                0                 1               1
## 11                    0                0                 1               0
## 12                    0                0                 0               0
## 13                    0                0                 0               0
## 14                    0                0                 0               1
## 15                    0                0                 0               0
## 16                    0                0                 0               0
## 17                    0                0                 0               1
## 18                    0                0                 1               0
## 19                    0                0                 1               0
## 20                    0                0                 1               1
## 21                    0                0                 1               0
## 22                    0                0                 0               0
## 23                    0                0                 0               0
## 24                    0                0                 0               0
## 25                    0                0                 0               0
## 26                    0                0                 1               0
## 27                    0                0                 0               0
## 28                    0                0                 1               0
## 29                    0                0                 0               0
## 30                    0                0                 0               0
## 31                    0                1                 0               0
## 32                    0                0                 1               0
## 33                    0                0                 0               0
## 34                    0                0                 0               1
## 35                    0                0                 0               0
## 36                    0                0                 0               0
## 37                    0                0                 0               0
## 38                    0                0                 0               0
## 39                    0                0                 0               1
## 40                    0                0                 0               0
## 41                    0                0                 2               0
## 42                    0                0                 0               0
## 43                    0                0                 1               0
## 44                    0                0                 1               0
## 45                    0                0                 0               0
## 46                    0                0                 0               0
## 47                    0                0                 0               0
## 48                    1                0                 0               0
## 49                    0                0                 1               0
## 50                    0                8                 1               0
##    Miconia.argentea Miconia.elata Miconia.hondurensis Mosannona.garwoodii
## 1                 2             0                   0                   1
## 2                 0             0                   0                   0
## 3                 1             0                   0                   0
## 4                 0             0                   0                   0
## 5                 1             0                   0                   1
## 6                 0             0                   0                   1
## 7                 1             0                   0                   1
## 8                 4             0                   0                   0
## 9                 0             0                   0                   0
## 10                0             0                   0                   1
## 11                0             0                   0                   0
## 12                0             0                   0                   0
## 13                5             0                   0                   0
## 14                3             0                   1                   0
## 15                0             0                   1                   0
## 16                0             0                   0                   0
## 17                3             0                   0                   2
## 18                4             0                   0                   1
## 19                0             1                   2                   0
## 20               10             0                   1                   1
## 21                0             0                   0                   0
## 22                0             0                   2                   1
## 23                0             0                   0                   0
## 24                6             0                   0                   0
## 25                0             0                   0                   0
## 26                0             0                   0                   0
## 27                2             0                   0                   0
## 28                0             0                   0                   0
## 29                2             0                   0                   0
## 30                8             0                   0                   0
## 31                0             0                   0                   1
## 32                1             0                   0                   0
## 33                0             0                   0                   0
## 34                3             0                   0                   0
## 35                3             0                   0                   0
## 36                0             0                   0                   0
## 37                2             0                   0                   0
## 38                1             0                   0                   0
## 39                1             0                   0                   0
## 40                0             0                   0                   0
## 41                1             0                   0                   0
## 42                0             0                   0                   0
## 43                0             0                   0                   0
## 44                0             0                   0                   1
## 45                0             0                   0                   1
## 46                3             0                   0                   1
## 47                3             0                   0                   1
## 48                0             0                   0                   0
## 49                0             0                   0                   0
## 50                0             0                   0                   0
##    Myrcia.gatunensis Myrospermum.frutescens Nectandra.cissiflora
## 1                  1                      0                    0
## 2                  0                      0                    1
## 3                  0                      0                    2
## 4                  0                      0                    2
## 5                  0                      0                    2
## 6                  0                      2                    0
## 7                  0                      0                    1
## 8                  0                      0                    2
## 9                  1                      0                    3
## 10                 0                      0                    5
## 11                 0                      0                    3
## 12                 0                      0                    0
## 13                 0                      0                    0
## 14                 1                      0                    1
## 15                 0                      0                    0
## 16                 0                      0                    0
## 17                 0                      0                    1
## 18                 0                      0                    0
## 19                 1                      0                    0
## 20                 0                      0                    2
## 21                 0                      0                    1
## 22                 0                      0                    0
## 23                 0                      0                    0
## 24                 0                      1                    0
## 25                 0                      0                    0
## 26                 0                      0                    0
## 27                 0                      0                    0
## 28                 0                      0                    1
## 29                 0                      0                    0
## 30                 0                      0                    0
## 31                 0                      1                    0
## 32                 0                      0                    0
## 33                 0                      0                    1
## 34                 0                      0                    0
## 35                 0                      0                    0
## 36                 0                      0                    0
## 37                 0                      0                    0
## 38                 0                      0                    0
## 39                 0                      0                    0
## 40                 0                      0                    0
## 41                 0                      0                    1
## 42                 0                      0                    3
## 43                 0                      0                    1
## 44                 0                      0                    0
## 45                 1                      0                    0
## 46                 0                      3                    0
## 47                 0                      0                    0
## 48                 0                      0                    0
## 49                 0                      0                    0
## 50                 0                      0                    0
##    Nectandra.lineata Nectandra.purpurea Ochroma.pyramidale Ocotea.cernua
## 1                  0                  1                  1             0
## 2                  0                  0                  0             0
## 3                  0                  0                  0             1
## 4                  0                  0                  0             1
## 5                  0                  0                  0             0
## 6                  0                  1                  0             0
## 7                  0                  0                  0             1
## 8                  0                  0                  3             0
## 9                  0                  0                  0             1
## 10                 0                  0                  0             0
## 11                 0                  0                  0             0
## 12                 1                  0                  0             2
## 13                 0                  0                  0             5
## 14                 0                  0                  0             1
## 15                 0                  0                  1             2
## 16                 1                  0                  0             0
## 17                 0                  0                  0             0
## 18                 1                  0                  0             1
## 19                 0                  0                  0             2
## 20                 1                  0                  0             1
## 21                 1                  0                  0             0
## 22                 0                  0                  0             0
## 23                 0                  0                  0             1
## 24                 1                  0                  0             1
## 25                 0                  0                  0             1
## 26                 0                  0                  0             0
## 27                 0                  0                  0             0
## 28                 0                  0                  0             0
## 29                 0                  0                  0             0
## 30                 0                  0                  0             1
## 31                 0                  0                  0             0
## 32                 0                  0                  0             0
## 33                 0                  0                  0             0
## 34                 0                  0                  0             2
## 35                 0                  0                  0             1
## 36                 1                  0                  0             0
## 37                 0                  0                  0             0
## 38                 0                  1                  0             0
## 39                 2                  0                  0             1
## 40                 0                  0                  0             0
## 41                 0                  0                  0             3
## 42                 0                  0                  0             0
## 43                 0                  0                  0             0
## 44                 0                  0                  0             0
## 45                 0                  0                  0             0
## 46                 0                  1                  0             0
## 47                 0                  0                  0             0
## 48                 0                  0                  0             0
## 49                 0                  0                  0             0
## 50                 1                  0                  0             0
##    Ocotea.oblonga Ocotea.puberula Ocotea.whitei Oenocarpus.mapora
## 1               0               0             1                22
## 2               0               0             0                21
## 3               1               0             2                14
## 4               2               2             3                23
## 5               0               0            16                17
## 6               0               1             3                19
## 7               0               0             0                20
## 8               0               2             1                20
## 9               0               0             1                18
## 10              1               2             3                20
## 11              3               1             3                17
## 12              0               0             0                19
## 13              0               3             0                17
## 14              1               0             1                22
## 15              1               3             1                11
## 16              0               0             2                15
## 17              0               0             0                31
## 18              0               0             0                24
## 19              0               1             1                24
## 20              0               2             5                19
## 21              2               0            12                11
## 22              1               0             0                24
## 23              0               0             0                22
## 24              0               1             2                24
## 25              1               1             1                14
## 26              0               0            15                 6
## 27              3               0             1                11
## 28              1               0             0                10
## 29              0               1             0                16
## 30              1               0             0                12
## 31              0               0            29                 7
## 32              2               0             4                 5
## 33              0               0             2                10
## 34              0               0             0                 9
## 35              1               0             0                 4
## 36              2               0            11                24
## 37              0               0             8                15
## 38              2               0             0                11
## 39              1               0             0                 4
## 40              1               0             0                 2
## 41              2               0             2                11
## 42              1               0             7                19
## 43              1               0             7                11
## 44              1               0             5                10
## 45              1               1            13                 8
## 46              0               0             0                36
## 47              1               0             1                28
## 48              1               1             4                15
## 49              1               0             8                 4
## 50              0               0             9                12
##    Ormosia.amazonica Ormosia.coccinea Ormosia.macrocalyx Pachira.quinata
## 1                  0                0                  0               0
## 2                  0                0                  0               0
## 3                  0                0                  0               0
## 4                  0                0                  0               0
## 5                  0                0                  0               0
## 6                  0                0                  0               0
## 7                  0                0                  0               1
## 8                  0                0                  0               0
## 9                  0                0                  0               0
## 10                 0                0                  0               0
## 11                 0                0                  0               0
## 12                 0                0                  1               0
## 13                 0                0                  0               0
## 14                 0                0                  0               0
## 15                 0                0                  0               0
## 16                 0                0                  0               0
## 17                 0                0                  0               0
## 18                 0                0                  0               0
## 19                 0                1                  0               0
## 20                 0                0                  0               0
## 21                 0                0                  0               0
## 22                 0                0                  0               0
## 23                 0                0                  0               0
## 24                 0                0                  0               0
## 25                 0                0                  0               0
## 26                 0                0                  0               0
## 27                 0                0                  1               0
## 28                 0                0                  0               0
## 29                 1                0                  0               0
## 30                 0                0                  0               0
## 31                 0                0                  0               0
## 32                 0                0                  0               0
## 33                 0                0                  1               0
## 34                 0                1                  0               0
## 35                 0                1                  0               0
## 36                 0                0                  0               0
## 37                 0                0                  0               0
## 38                 0                0                  0               0
## 39                 0                1                  0               0
## 40                 0                0                  0               0
## 41                 0                0                  0               0
## 42                 0                0                  0               0
## 43                 0                0                  0               0
## 44                 0                1                  0               0
## 45                 0                0                  0               0
## 46                 0                0                  0               0
## 47                 0                0                  0               0
## 48                 0                0                  0               0
## 49                 0                0                  0               0
## 50                 0                0                  0               0
##    Pachira.sessilis Perebea.xanthochyma Cinnamomum.triplinerve
## 1                 0                   0                      0
## 2                 0                   1                      0
## 3                 0                   0                      1
## 4                 0                   0                      0
## 5                 0                   1                      1
## 6                 0                   0                      0
## 7                 0                   0                      2
## 8                 0                   0                      0
## 9                 0                   8                      1
## 10                0                   6                      0
## 11                0                   0                      0
## 12                0                   0                      1
## 13                0                   0                      0
## 14                0                   2                      1
## 15                0                   1                      0
## 16                0                   0                      1
## 17                0                   0                      0
## 18                0                   0                      0
## 19                0                   0                      0
## 20                0                   1                      0
## 21                0                   0                      0
## 22                0                   0                      1
## 23                0                   0                      1
## 24                0                   0                      2
## 25                0                   0                      1
## 26                0                   0                      0
## 27                0                   0                      0
## 28                0                   0                      0
## 29                0                   0                      0
## 30                9                   0                      0
## 31                0                   0                      0
## 32                0                   0                      0
## 33                0                   0                      0
## 34                0                   0                      0
## 35                0                   0                      1
## 36                0                   1                      1
## 37                0                   0                      0
## 38                0                   0                      0
## 39                0                   0                      0
## 40                0                   0                      0
## 41                0                   0                      1
## 42                0                   0                      0
## 43                0                   0                      0
## 44                0                   0                      0
## 45                0                   0                      0
## 46                0                   0                      0
## 47                0                   0                      0
## 48                0                   0                      0
## 49                0                   0                      0
## 50                0                   0                      0
##    Picramnia.latifolia Piper.reticulatum Platymiscium.pinnatum
## 1                    0                 0                     3
## 2                    0                 0                     3
## 3                    1                 0                     5
## 4                    0                 0                     1
## 5                    0                 2                     1
## 6                    0                 0                     1
## 7                    0                 0                     6
## 8                    1                 0                     0
## 9                    0                 0                     2
## 10                   0                 0                     0
## 11                   1                 1                     0
## 12                   0                 0                     0
## 13                   1                 0                     2
## 14                   1                 0                     2
## 15                   0                 0                     1
## 16                   0                 0                     1
## 17                   0                 1                     2
## 18                   0                 0                     1
## 19                   0                 0                     2
## 20                   1                 0                     0
## 21                   0                 0                     0
## 22                   1                 0                     0
## 23                   0                 0                     1
## 24                   0                 0                     2
## 25                   1                 0                     3
## 26                   6                 1                     1
## 27                   3                 1                     0
## 28                   0                 0                     4
## 29                   0                 0                     0
## 30                   0                 0                     0
## 31                   2                 0                     0
## 32                   2                 0                     2
## 33                   0                 0                     0
## 34                   2                 1                     2
## 35                   1                 0                     1
## 36                   2                 1                     0
## 37                   2                 0                     2
## 38                   1                 0                     1
## 39                   0                 0                     0
## 40                   0                 0                     0
## 41                   5                 0                     0
## 42                   1                 0                     2
## 43                   0                 0                     1
## 44                   1                 0                     1
## 45                   1                 0                     2
## 46                   2                 0                     2
## 47                   0                 0                     1
## 48                   4                 1                     0
## 49                   1                 0                     0
## 50                   1                 0                     0
##    Platypodium.elegans Posoqueria.latifolia Poulsenia.armata Pourouma.bicolor
## 1                    2                    0               24                5
## 2                    1                    1               16                3
## 3                    3                    0               28                0
## 4                    0                    0               15                0
## 5                    0                    0               25                1
## 6                    2                    0               15                0
## 7                    3                    0                8                0
## 8                    3                    0               13                1
## 9                    1                    0                5                1
## 10                   0                    0               24                0
## 11                   1                    0               22                1
## 12                   2                    0                8                0
## 13                   2                    0                0                0
## 14                   1                    0               13                0
## 15                   2                    0               16                0
## 16                   1                    0               32                0
## 17                   0                    1                2                0
## 18                   1                    0                0                0
## 19                   1                    0                4                0
## 20                   1                    0               15                0
## 21                   0                    0               44                0
## 22                   0                    0                5                0
## 23                   1                    3                1                0
## 24                   0                    0                6                0
## 25                   1                    1                4                0
## 26                   2                    0               22                0
## 27                   1                    1                9                0
## 28                   2                    0                1                0
## 29                   0                    0                2                0
## 30                   1                    0                8                0
## 31                   0                    0               24                0
## 32                   1                    0                2                0
## 33                   0                    0                4                0
## 34                   0                    0                1                0
## 35                   1                    0                0                0
## 36                   1                    0               14                0
## 37                   0                    0                6                0
## 38                   0                    0                1                0
## 39                   0                    0                1                0
## 40                   2                    0                2                0
## 41                   0                    1               11                0
## 42                   0                    0               26                0
## 43                   0                    0               55                0
## 44                   1                    0               55                0
## 45                   0                    1               57                1
## 46                   0                    3                0                0
## 47                   2                    0                4                0
## 48                   0                    3               23                0
## 49                   0                    0               39                0
## 50                   0                    0               43                0
##    Pouteria.fossicola Pouteria.reticulata Pouteria.stipitata Prioria.copaifera
## 1                   0                   5                  0                13
## 2                   0                   7                  0                12
## 3                   0                   3                  1                12
## 4                   0                   6                  0                 5
## 5                   0                   5                  0                 3
## 6                   0                   4                  0                26
## 7                   0                   4                  0                18
## 8                   0                   4                  0                 5
## 9                   0                   3                  0                 1
## 10                  0                   0                  1                 2
## 11                  0                   5                  1                26
## 12                  0                   4                  0                21
## 13                  0                   5                  0                 7
## 14                  0                   5                  1                 3
## 15                  0                   4                  0                 0
## 16                  0                   3                  1                18
## 17                  0                   5                  6                25
## 18                  0                  17                  1                 5
## 19                  0                  10                  5                 5
## 20                  0                   1                  2                 0
## 21                  1                   1                  0                14
## 22                  0                   2                  1                17
## 23                  0                   6                  0                 1
## 24                  1                   4                  0                 4
## 25                  0                   9                  0                 1
## 26                  0                   3                  0                11
## 27                  0                   2                  1                11
## 28                  0                   2                  0                 4
## 29                  0                   2                  1                14
## 30                  0                   3                  1                 9
## 31                  0                   3                  0                 3
## 32                  0                   4                  0                 1
## 33                  0                   3                  1                 5
## 34                  0                   3                  0                14
## 35                  0                   4                  0                 7
## 36                  0                   3                  1                 0
## 37                  0                   2                  0                 1
## 38                  0                   4                  0                 5
## 39                  0                   4                  0                 6
## 40                  0                   5                  0                 1
## 41                  0                   3                  0                 0
## 42                  0                   4                  0                 1
## 43                  0                   4                  0                 1
## 44                  0                   2                  0                 1
## 45                  0                   2                  1                 0
## 46                  0                   4                  3                 3
## 47                  0                   7                  1                 1
## 48                  0                   5                  0                 2
## 49                  0                   2                  1                 0
## 50                  0                   1                  0                 0
##    Protium.costaricense Protium.panamense Protium.tenuifolium
## 1                     5                 2                  11
## 2                     4                 0                   8
## 3                     1                 2                   3
## 4                     3                 3                   9
## 5                     7                 2                   3
## 6                     1                 1                   2
## 7                     0                 0                   6
## 8                     0                 3                   7
## 9                     4                 0                   4
## 10                    4                 1                   6
## 11                    2                 0                   4
## 12                    0                 0                   5
## 13                    0                 0                   4
## 14                    3                 4                   5
## 15                    4                 0                   4
## 16                    1                 0                   2
## 17                    1                 1                   2
## 18                    0                 0                   1
## 19                    0                 2                   5
## 20                    7                 0                   9
## 21                    2                 1                   7
## 22                    0                 2                   4
## 23                    0                 2                   3
## 24                    0                 1                   7
## 25                    6                 4                   7
## 26                    4                 0                   6
## 27                    2                 1                   4
## 28                    3                 1                   2
## 29                    1                 1                   6
## 30                    4                 2                   9
## 31                    3                 0                   9
## 32                    2                 1                   3
## 33                    1                 0                   8
## 34                    5                 3                   8
## 35                    1                 0                   1
## 36                    3                 0                   3
## 37                    4                 0                   8
## 38                    1                 0                  10
## 39                    3                 1                  10
## 40                    2                 0                   7
## 41                    0                 1                   6
## 42                    3                 2                  12
## 43                    1                 0                   6
## 44                    3                 2                   8
## 45                    1                 3                  11
## 46                    0                 0                  18
## 47                    1                 1                  27
## 48                    1                 0                  26
## 49                    2                 0                  22
## 50                    5                 0                  23
##    Pseudobombax.septenatum Psidium.friedrichsthalianum Psychotria.grandis
## 1                        0                           0                  0
## 2                        0                           0                  0
## 3                        0                           0                  0
## 4                        0                           0                  0
## 5                        0                           0                  0
## 6                        0                           0                  0
## 7                        0                           0                  0
## 8                        0                           0                  0
## 9                        0                           0                  0
## 10                       0                           0                  0
## 11                       0                           0                  0
## 12                       0                           0                  0
## 13                       0                           1                  0
## 14                       0                           0                  0
## 15                       0                           0                  0
## 16                       0                           0                  0
## 17                       0                           0                  0
## 18                       0                           0                  0
## 19                       0                           0                  0
## 20                       0                           0                  0
## 21                       1                           0                  0
## 22                       0                           0                  0
## 23                       1                           0                  2
## 24                       1                           0                  0
## 25                       0                           0                  0
## 26                       0                           1                  0
## 27                       1                           0                  0
## 28                       1                           0                  0
## 29                       0                           0                  0
## 30                       1                           0                  0
## 31                       0                           0                  0
## 32                       0                           0                  0
## 33                       0                           1                  0
## 34                       0                           0                  0
## 35                       2                           0                  0
## 36                       0                           0                  0
## 37                       0                           0                  0
## 38                       0                           0                  0
## 39                       0                           0                  0
## 40                       0                           0                  0
## 41                       0                           0                  0
## 42                       0                           0                  0
## 43                       0                           1                  0
## 44                       0                           0                  0
## 45                       0                           0                  0
## 46                       0                           0                  0
## 47                       0                           0                  0
## 48                       0                           0                  0
## 49                       0                           0                  0
## 50                       0                           0                  0
##    Pterocarpus.rohrii Quararibea.asterolepis Quassia.amara Randia.armata
## 1                   1                     11             0             3
## 2                   0                     12             0             2
## 3                   0                     15             0             1
## 4                   2                     14             0             4
## 5                   1                      9             0             2
## 6                   1                      3             0             9
## 7                   2                     21             0            14
## 8                   2                      7             0             4
## 9                   1                      4             0             4
## 10                  0                     18             0             1
## 11                  2                     25             0             7
## 12                  2                     11             0             2
## 13                  2                      1             0            15
## 14                  2                     10             0             3
## 15                  2                      8             0             2
## 16                  1                     25             0             3
## 17                  1                      9             0             5
## 18                  3                      0             0            10
## 19                  1                      2             0             2
## 20                  3                     15             0             3
## 21                  0                     12             0             1
## 22                  0                     11             0            11
## 23                  4                      6             0             1
## 24                  0                     12             0             4
## 25                  1                     22             0             4
## 26                  2                     20             0             3
## 27                  1                     20             0            10
## 28                  2                     24             0             5
## 29                  1                     14             0             6
## 30                  3                     13             0             4
## 31                  1                     25             0             7
## 32                  6                     21             0            20
## 33                  1                     22             0            16
## 34                  1                     17             0            11
## 35                  2                     11             0             5
## 36                  0                     11             0             2
## 37                  3                     14             1             2
## 38                  2                     20             0             8
## 39                  2                     20             0             5
## 40                  0                     22             0             7
## 41                  2                     11             0             3
## 42                  3                     19             0             1
## 43                  1                     12             0             2
## 44                  1                     23             0             1
## 45                  1                     32             0             1
## 46                  3                      3             3             4
## 47                  1                      7             0             2
## 48                  2                     21             0             4
## 49                  3                     25             0             0
## 50                  2                     14             0             2
##    Sapium.broadleaf Sapium.glandulosum Schizolobium.parahyba Senna.dariensis
## 1                 0                  0                     0               0
## 2                 0                  0                     0               0
## 3                 0                  1                     0               0
## 4                 0                  0                     0               0
## 5                 0                  2                     0               0
## 6                 0                  0                     1               0
## 7                 0                  0                     0               0
## 8                 0                  0                     0               0
## 9                 0                  0                     0               0
## 10                0                  0                     0               0
## 11                0                  0                     0               0
## 12                0                  0                     0               0
## 13                0                  0                     0               0
## 14                0                  0                     0               0
## 15                0                  0                     0               0
## 16                0                  0                     0               0
## 17                0                  0                     0               0
## 18                0                  1                     0               0
## 19                0                  1                     0               0
## 20                0                  0                     0               0
## 21                0                  0                     0               0
## 22                0                  0                     1               0
## 23                0                  0                     0               0
## 24                0                  1                     0               0
## 25                0                  1                     0               0
## 26                0                  1                     0               0
## 27                0                  2                     0               0
## 28                0                  0                     0               0
## 29                0                  0                     0               0
## 30                0                  0                     0               0
## 31                0                  0                     0               0
## 32                0                  0                     0               0
## 33                0                  1                     0               0
## 34                0                  1                     0               0
## 35                0                  1                     0               0
## 36                0                  0                     0               0
## 37                0                  0                     0               0
## 38                0                  0                     0               0
## 39                0                  0                     0               0
## 40                0                  0                     0               0
## 41                0                  0                     0               1
## 42                0                  0                     0               0
## 43                1                  0                     0               0
## 44                1                  0                     0               0
## 45                1                  0                     0               0
## 46                0                  1                     0               0
## 47                0                  0                     0               0
## 48                0                  1                     0               0
## 49                0                  1                     0               0
## 50                0                  1                     0               0
##    Simarouba.amara Siparuna.guianensis Siparuna.pauciflora Sloanea.terniflora
## 1               14                   3                   0                  1
## 2                6                   2                   0                  0
## 3               16                   1                   1                  2
## 4                8                   2                   0                  2
## 5                7                   0                   3                  3
## 6                7                   1                   0                  2
## 7               13                   1                   0                  1
## 8               14                   0                   0                  2
## 9               12                   0                   1                  1
## 10              17                   0                   1                  2
## 11               7                   1                   0                  1
## 12               9                   0                   0                  1
## 13               2                   0                   0                  1
## 14               4                   0                   0                  1
## 15               6                   0                   2                  0
## 16               8                   1                   0                  0
## 17               2                   0                   0                  1
## 18               2                   1                   0                  0
## 19               6                   0                   1                  1
## 20               8                   0                   0                  0
## 21               4                   0                   0                  1
## 22               5                   0                   0                  0
## 23               1                   0                   0                  0
## 24               3                   0                   1                  0
## 25              10                   0                   0                  0
## 26               5                   0                   0                  1
## 27              16                   0                   0                  0
## 28               7                   0                   0                  1
## 29               3                   0                   0                  1
## 30               8                   0                   1                  1
## 31               5                   0                   1                  2
## 32               5                   0                   0                  2
## 33               2                   0                   0                  2
## 34               2                   0                   0                  1
## 35               0                   0                   0                  0
## 36               9                   0                   0                  3
## 37               6                   0                   1                  3
## 38               3                   0                   0                  4
## 39               1                   0                   0                  1
## 40               4                   0                   1                  1
## 41               1                   0                   0                  1
## 42               4                   0                   0                  7
## 43               0                   0                   1                  2
## 44               0                   0                   0                  1
## 45               3                   0                   0                  5
## 46               3                   0                   0                  2
## 47               4                   0                   0                  4
## 48               0                   0                   0                  3
## 49               4                   0                   0                  2
## 50               3                   0                   1                  5
##    Socratea.exorrhiza Solanum.hayesii Sorocea.affinis Spachea.membranacea
## 1                  15               0               1                   0
## 2                  22               0               1                   0
## 3                  31               0               1                   0
## 4                   9               0               1                   0
## 5                  55               1               0                   0
## 6                  44               0               1                   0
## 7                  23               0               0                   0
## 8                  22               0               0                   0
## 9                  17               0               0                   0
## 10                 12               2               1                   0
## 11                  5               0               1                   0
## 12                  8               0               0                   0
## 13                  0               0               0                   0
## 14                  6               0               0                   0
## 15                  7               1               1                   0
## 16                  1               2               0                   0
## 17                  0               0               0                   0
## 18                  0               0               0                   0
## 19                  3               0               1                   0
## 20                  6               0               0                   1
## 21                  5               1               0                   0
## 22                  0               0               0                   0
## 23                  1               1               1                   0
## 24                  5               0               1                   0
## 25                  5               0               0                   7
## 26                  3               0               0                   0
## 27                  0               1               2                   0
## 28                  0               0               1                   0
## 29                  0               0               1                   0
## 30                  0               0               0                   0
## 31                  8               0               2                   0
## 32                  0               1               1                   0
## 33                  0               0               0                   0
## 34                  0               0               0                   0
## 35                  0               1               0                   0
## 36                  1               1               0                   0
## 37                  0               0               0                   0
## 38                  2               0               0                   0
## 39                  0               0               0                   0
## 40                  0               0               0                   0
## 41                  0               0               0                   0
## 42                  3               0               0                   0
## 43                  7               0               1                   0
## 44                  5               0               0                   0
## 45                  9               0               1                   0
## 46                  0               0               0                   0
## 47                  0               0               3                   0
## 48                  0               0               2                   0
## 49                  2               0               3                   0
## 50                  4               0               0                   0
##    Spondias.mombin Spondias.radlkoferi Sterculia.apetala
## 1                1                   2                 1
## 2                1                   0                 2
## 3                0                   3                 0
## 4                1                   3                 0
## 5                1                   5                 0
## 6                0                   0                 1
## 7                0                   5                 1
## 8                1                   0                 0
## 9                0                   1                 0
## 10               2                   1                 0
## 11               0                   1                 0
## 12               1                   0                 0
## 13              10                   1                 3
## 14               1                   0                 0
## 15               0                   2                 0
## 16               0                   2                 0
## 17               1                   0                 1
## 18               3                   3                 2
## 19               0                   0                 1
## 20               0                   3                 0
## 21               0                   1                 0
## 22               0                   1                 0
## 23               2                   2                 1
## 24               0                   1                 0
## 25               0                   2                 0
## 26               0                   0                 1
## 27               0                   0                 0
## 28               0                   0                 1
## 29               0                   2                 0
## 30               1                   1                 1
## 31               0                   1                 0
## 32               0                   1                 2
## 33               0                   0                 0
## 34               0                   1                 0
## 35               0                   1                 0
## 36               0                   3                 0
## 37               0                   1                 1
## 38               0                   0                 0
## 39               0                   1                 0
## 40               0                   2                 0
## 41               0                   3                 1
## 42               0                   1                 1
## 43               0                   1                 1
## 44               0                   0                 0
## 45               0                   0                 1
## 46               0                   1                 2
## 47               0                   0                 1
## 48               1                   2                 0
## 49               1                   1                 0
## 50               1                   1                 0
##    Swartzia.simplex.var.grandiflora Swartzia.simplex.continentalis
## 1                                 3                              1
## 2                                 3                              4
## 3                                 0                              2
## 4                                 1                              2
## 5                                 1                              1
## 6                                 9                              5
## 7                                 9                              7
## 8                                 5                              0
## 9                                 5                              0
## 10                                0                              0
## 11                               10                              5
## 12                               13                             13
## 13                                2                              2
## 14                                3                              3
## 15                                1                              0
## 16                                5                              5
## 17                                6                              4
## 18                                9                              2
## 19                                6                              4
## 20                                2                              0
## 21                                2                              1
## 22                                6                              4
## 23                                2                              4
## 24                                4                              3
## 25                                2                              1
## 26                                5                              2
## 27                                6                              4
## 28                                8                              1
## 29                                6                              4
## 30                                3                              0
## 31                                0                              1
## 32                                4                              3
## 33                               13                              4
## 34                               14                              2
## 35                                4                              1
## 36                                0                              3
## 37                                8                              3
## 38                               10                              2
## 39                                5                              3
## 40                                1                              3
## 41                                0                              0
## 42                                3                              1
## 43                                8                              0
## 44                                3                              2
## 45                                1                              1
## 46                                0                              0
## 47                                0                              1
## 48                                4                              2
## 49                                2                              1
## 50                                1                              1
##    Symphonia.globulifera Handroanthus.guayacan Tabebuia.rosea
## 1                      0                     1              1
## 2                      1                     0              2
## 3                      1                     1              1
## 4                      1                     0              2
## 5                      2                     0              3
## 6                      0                     1              0
## 7                      0                     0              1
## 8                      1                     0              0
## 9                      1                     0              0
## 10                     0                     0              0
## 11                     0                     0              0
## 12                     1                     0              0
## 13                     0                     2              6
## 14                     0                     1              0
## 15                     2                     1              0
## 16                     1                     0              1
## 17                     0                     1              1
## 18                     0                     0              0
## 19                     0                     0              0
## 20                     0                     0              1
## 21                     2                     0              2
## 22                     0                     2              0
## 23                     0                     0              4
## 24                     1                     1              0
## 25                     1                     0              0
## 26                     0                     0              2
## 27                     0                     2              0
## 28                     0                     6              1
## 29                     0                     1              0
## 30                     0                     4              3
## 31                     0                     0              2
## 32                     0                     0              1
## 33                     0                     0              5
## 34                     0                     0              0
## 35                     0                     1              0
## 36                     0                     0              2
## 37                     0                     0              1
## 38                     0                     0              1
## 39                     1                     0              4
## 40                     0                     0              2
## 41                     2                     0              1
## 42                     1                     0              1
## 43                     0                     2              0
## 44                     0                     1              2
## 45                     2                     0              1
## 46                     0                     1              3
## 47                     1                     0              3
## 48                     0                     0              5
## 49                     1                     0              2
## 50                     3                     1              1
##    Tabernaemontana.arborea Tachigali.versicolor Talisia.nervosa
## 1                        9                    6               0
## 2                        5                    1               0
## 3                        6                    3               0
## 4                       10                    3               0
## 5                       16                    0               0
## 6                       11                    1               0
## 7                        9                    2               0
## 8                        8                    0               0
## 9                       12                    3               0
## 10                      10                    1               0
## 11                       4                    4               0
## 12                       6                    2               0
## 13                      12                    3               1
## 14                      22                    0               0
## 15                       8                    5               0
## 16                      11                    2               0
## 17                       3                    1               0
## 18                      10                    3               0
## 19                       9                    2               0
## 20                      13                    3               0
## 21                       4                    1               0
## 22                      10                    1               0
## 23                       5                    1               0
## 24                       9                    3               0
## 25                       6                    3               0
## 26                       4                    4               0
## 27                      12                    2               0
## 28                       5                    8               0
## 29                       2                    2               0
## 30                      21                    1               0
## 31                       1                    5               0
## 32                       4                    1               0
## 33                       2                    1               0
## 34                       5                    0               0
## 35                       2                    1               0
## 36                       1                    1               0
## 37                       0                    1               0
## 38                       4                    1               0
## 39                       3                    2               0
## 40                       2                    0               0
## 41                       1                    3               0
## 42                       2                    1               0
## 43                       0                    2               0
## 44                       1                    0               0
## 45                       2                    2               0
## 46                       2                    1               0
## 47                       1                    1               0
## 48                       8                    0               0
## 49                       2                    2               0
## 50                       7                    2               0
##    Talisia.princeps Terminalia.amazonia Terminalia.oblonga
## 1                 1                   1                  0
## 2                 0                   0                  0
## 3                 0                   0                  0
## 4                 0                   0                  0
## 5                 0                   1                  0
## 6                 0                   1                  0
## 7                 0                   0                  0
## 8                 0                   0                  0
## 9                 0                   0                  0
## 10                0                   0                  0
## 11                0                   0                  0
## 12                0                   0                  0
## 13                0                   5                  0
## 14                0                   2                  0
## 15                0                   0                  0
## 16                0                   0                  3
## 17                0                   0                  0
## 18                0                   2                  0
## 19                0                   0                  0
## 20                0                   1                  0
## 21                0                   0                  1
## 22                0                   0                  1
## 23                0                   6                  0
## 24                0                   1                  0
## 25                0                   2                  2
## 26                1                   0                  5
## 27                0                   0                 10
## 28                1                   0                  0
## 29                0                   1                  0
## 30                0                   0                  0
## 31                0                   1                  8
## 32                0                   0                  2
## 33                0                   0                  0
## 34                0                   0                  0
## 35                0                   2                  0
## 36                0                   0                  0
## 37                0                   0                  0
## 38                0                   0                  0
## 39                0                   0                  0
## 40                0                   1                  0
## 41                0                   0                  0
## 42                0                   0                  0
## 43                0                   0                  0
## 44                0                   0                  0
## 45                0                   0                  0
## 46                0                   0                  0
## 47                0                   0                  0
## 48                0                   0                  2
## 49                0                   1                  9
## 50                0                   0                  0
##    Tetragastris.panamensis Tetrathylacium.johansenii Theobroma.cacao
## 1                        5                         0               1
## 2                        7                         0               1
## 3                       10                         0               0
## 4                       10                         0               0
## 5                        7                         0               1
## 6                       17                         0               0
## 7                        8                         0               0
## 8                        9                         0               0
## 9                        5                         0               0
## 10                       6                         0               0
## 11                      10                         0               0
## 12                      10                         0               0
## 13                       6                         0               0
## 14                       5                         0               0
## 15                       3                         0               0
## 16                       6                         0               1
## 17                      13                         0               0
## 18                      11                         2               0
## 19                       9                         0               0
## 20                       4                         0               0
## 21                       4                         0               0
## 22                       9                         0               0
## 23                      11                         2               0
## 24                      15                         0               1
## 25                       7                         0               1
## 26                       6                         0               0
## 27                      11                         1               0
## 28                      13                         0               0
## 29                       8                         0               1
## 30                       5                         1               0
## 31                       5                         0               0
## 32                       4                         0               1
## 33                       1                         0               0
## 34                       2                         1               0
## 35                       1                         0               0
## 36                       5                         0               0
## 37                       9                         0               0
## 38                       1                         0               0
## 39                       2                         0               0
## 40                       1                         0               0
## 41                       7                         0               1
## 42                       7                         0               0
## 43                       6                         0               1
## 44                       4                         0               0
## 45                       9                         0               0
## 46                      20                         0               0
## 47                      25                         0               0
## 48                       8                         0               0
## 49                       4                         0               0
## 50                       8                         0               2
##    Thevetia.ahouai Tocoyena.pittieri Trattinnickia.aspera Trema.micrantha
## 1                0                 0                    3               0
## 2                0                 1                    1               0
## 3                0                 0                    1               0
## 4                0                 0                    0               2
## 5                0                 0                    2               1
## 6                0                 0                    0               0
## 7                0                 0                    0               0
## 8                0                 0                    2               0
## 9                0                 0                    2               0
## 10               0                 0                    1               0
## 11               0                 0                    0               1
## 12               0                 1                    0               1
## 13               0                 0                    0               0
## 14               0                 0                    0               0
## 15               0                 0                    1               0
## 16               0                 0                    1               0
## 17               0                 0                    3               0
## 18               0                 0                    0               0
## 19               0                 0                    3               1
## 20               0                 0                    0               0
## 21               0                 1                    1               0
## 22               0                 0                    0               0
## 23               1                 0                    0               1
## 24               0                 0                    1               0
## 25               0                 0                    0               1
## 26               0                 0                    0               0
## 27               0                 0                    1               0
## 28               0                 0                    1               1
## 29               0                 0                    0               0
## 30               0                 0                    0               0
## 31               0                 0                    0               0
## 32               0                 0                    0               0
## 33               0                 1                    0               0
## 34               0                 0                    0               0
## 35               0                 0                    0               0
## 36               0                 0                    4               0
## 37               0                 0                    1               0
## 38               0                 0                    0               0
## 39               0                 0                    0               3
## 40               0                 0                    1               0
## 41               1                 0                    0               0
## 42               0                 0                    0               1
## 43               0                 0                    0               0
## 44               0                 0                    0               1
## 45               0                 0                    0               0
## 46               0                 0                    7               0
## 47               0                 0                    1               0
## 48               0                 0                    1               0
## 49               0                 0                    0               0
## 50               0                 1                    1               1
##    Trichanthera.gigantea Trichilia.pallida Trichilia.tuberculata
## 1                      0                 0                    18
## 2                      0                 1                    27
## 3                      0                 0                    28
## 4                      0                 1                    35
## 5                      0                 0                    15
## 6                      0                 0                    31
## 7                      0                 1                    27
## 8                      0                 0                    36
## 9                      0                 0                    65
## 10                     0                 0                    46
## 11                     0                 2                    41
## 12                     0                 1                    46
## 13                     0                 8                    35
## 14                     0                 1                    33
## 15                     0                 6                    33
## 16                     0                 3                    25
## 17                     0                 2                    36
## 18                     0                 5                    23
## 19                     0                 1                    44
## 20                     0                10                    33
## 21                     0                 0                    23
## 22                     0                 1                    42
## 23                     0                 1                    23
## 24                     1                 2                    38
## 25                     1                 6                    26
## 26                     0                 1                    15
## 27                     0                 3                    20
## 28                     0                 0                    43
## 29                     0                 0                    47
## 30                     0                 4                    33
## 31                     0                 1                    33
## 32                     0                 8                    50
## 33                     0                 1                    37
## 34                     0                 2                    31
## 35                     0                 1                    30
## 36                     0                 0                    28
## 37                     0                 4                    33
## 38                     0                 1                    59
## 39                     0                 0                    79
## 40                     0                 2                    97
## 41                     0                 0                    19
## 42                     0                 0                    15
## 43                     0                 0                    36
## 44                     0                 0                    26
## 45                     0                 0                    26
## 46                     0                 0                    16
## 47                     0                 1                    16
## 48                     0                 0                    19
## 49                     0                 1                    26
## 50                     0                 0                    18
##    Trichospermum.galeottii Triplaris.cumingiana Trophis.caucana
## 1                        0                    0               2
## 2                        0                    0               0
## 3                        0                    0               0
## 4                        0                    0               0
## 5                        0                    0               2
## 6                        0                    1               0
## 7                        0                    0               0
## 8                        0                    0               0
## 9                        0                    0               0
## 10                       0                    1               0
## 11                       0                    1               2
## 12                       0                    3               0
## 13                       0                   13               0
## 14                       0                    7               0
## 15                       0                    0               0
## 16                       0                    2               0
## 17                       0                    3               1
## 18                       0                    6               0
## 19                       0                    1               0
## 20                       1                    0               0
## 21                       0                    2               1
## 22                       0                    1               1
## 23                       0                   11               0
## 24                       0                    1               0
## 25                       0                    3               0
## 26                       0                    2               1
## 27                       0                    3               0
## 28                       0                    0               0
## 29                       0                    0               0
## 30                       0                    0               0
## 31                       0                    1               0
## 32                       0                   13               0
## 33                       0                   11               0
## 34                       0                   11               0
## 35                       0                    1               0
## 36                       0                    0               0
## 37                       0                    3               0
## 38                       0                    6               0
## 39                       0                    4               0
## 40                       0                    5               0
## 41                       0                    1               0
## 42                       0                    0               0
## 43                       0                    1               4
## 44                       0                    6               1
## 45                       0                    5               4
## 46                       0                    1               0
## 47                       0                    3               0
## 48                       0                    6               3
## 49                       0                    4               8
## 50                       0                    4               3
##    Trophis.racemosa Turpinia.occidentalis Unonopsis.pittieri Virola.multiflora
## 1                 1                     0                  1                 0
## 2                 1                     1                  5                 0
## 3                 0                     1                 12                 0
## 4                 1                     4                  3                 0
## 5                 0                     2                  4                 0
## 6                 0                     1                  3                 2
## 7                 1                     0                  3                 0
## 8                 0                     1                  2                 0
## 9                 0                     1                  5                 0
## 10                2                     1                  9                 1
## 11                0                     1                  4                 0
## 12                0                     1                  0                 1
## 13                0                     0                  0                 0
## 14                1                     0                  3                 0
## 15                0                     5                 11                 0
## 16                2                     2                  1                 1
## 17                0                     0                  0                 0
## 18                2                     0                  0                 0
## 19                3                     0                  4                 0
## 20                0                     5                 10                 0
## 21                0                     1                  6                 2
## 22                0                     1                  1                 0
## 23                1                     0                  1                 0
## 24                1                     2                  3                 0
## 25                2                     0                  3                 0
## 26                1                     0                  4                 1
## 27                1                     7                  0                 0
## 28                0                     1                  0                 0
## 29                0                     3                  5                 0
## 30                2                     1                  1                 1
## 31                1                     0                  3                 5
## 32                2                     0                  4                 0
## 33                1                     2                  5                 0
## 34                0                     1                  1                 0
## 35                0                     0                  0                 0
## 36                0                     2                  9                 2
## 37                0                     5                  8                 2
## 38                0                     0                  2                 0
## 39                0                     2                  0                 0
## 40                1                     1                  0                 0
## 41                0                     2                  4                 2
## 42                0                     0                  5                 3
## 43                1                     0                  5                 0
## 44                0                     0                  3                 0
## 45                0                     0                  4                 0
## 46                0                     0                  0                 0
## 47                2                     0                  0                 0
## 48                2                     0                  0                 1
## 49                0                     0                  2                 0
## 50                0                     1                  4                 1
##    Virola.sebifera Virola.surinamensis Vismia.baccifera Vochysia.ferruginea
## 1               17                   4                0                   0
## 2               12                   3                0                   0
## 3               11                   2                0                   0
## 4               16                   2                0                   0
## 5               31                   6                0                   0
## 6               19                   1                0                   0
## 7                8                   1                0                   0
## 8               19                   1                0                   0
## 9               16                   1                0                   0
## 10              17                   2                0                   0
## 11               6                   4                0                   0
## 12               6                   2                0                   2
## 13               0                   0                0                   3
## 14              17                   1                0                   1
## 15              16                   4                0                   0
## 16              24                   5                0                   0
## 17               5                   0                0                   1
## 18               0                   2                0                   2
## 19              12                   1                0                   0
## 20              15                   4                0                   0
## 21              15                  10                0                   0
## 22               7                   1                0                   0
## 23               9                   1                0                   0
## 24              12                   1                0                   0
## 25              12                   4                0                   0
## 26              20                  12                0                   0
## 27              12                   1                0                   0
## 28              18                   1                0                   0
## 29               9                   1                0                   0
## 30               8                   3                0                   0
## 31              20                   6                0                   0
## 32              18                   4                0                   0
## 33              16                   3                0                   0
## 34               7                   1                0                   0
## 35              11                   0                0                   0
## 36              14                   5                0                   0
## 37              14                   4                1                   0
## 38              11                   0                0                   0
## 39               7                   2                0                   0
## 40              11                   1                0                   0
## 41              12                   7                0                   0
## 42              12                   5                0                   0
## 43              14                   8                0                   0
## 44              10                   1                0                   0
## 45              13                   7                0                   0
## 46               0                   0                0                   2
## 47              11                   1                0                   1
## 48               7                   5                0                   0
## 49               6                  16                0                   0
## 50              14                   7                0                   0
##    Xylopia.macrantha Zanthoxylum.ekmanii Zanthoxylum.juniperinum
## 1                  1                   3                       0
## 2                  0                   4                       0
## 3                  0                   8                       1
## 4                  0                  13                       1
## 5                  0                   3                       0
## 6                  0                   1                       0
## 7                  0                   2                       0
## 8                  0                   4                       0
## 9                  0                  13                       1
## 10                 4                   7                      10
## 11                 1                   1                       0
## 12                 0                   0                       0
## 13                 1                   5                       2
## 14                 0                  12                       3
## 15                 3                   5                       6
## 16                 1                   2                       1
## 17                 2                   1                       0
## 18                 1                   0                       2
## 19                 1                   3                       1
## 20                 1                   4                       2
## 21                15                   7                       2
## 22                 0                   1                       1
## 23                 0                   0                       0
## 24                 0                   0                       0
## 25                 0                   4                       3
## 26                15                   1                       1
## 27                 8                   4                       1
## 28                 0                   0                       0
## 29                 0                   2                       0
## 30                 0                   1                       0
## 31                23                   0                       1
## 32                 4                   4                       0
## 33                 8                   3                       0
## 34                 1                   0                       0
## 35                 0                   0                       0
## 36                20                   2                       1
## 37                 1                   5                       0
## 38                 1                   2                       1
## 39                 0                   1                       1
## 40                 0                   0                       0
## 41                 9                   3                       0
## 42                14                   4                       0
## 43                 2                   1                       0
## 44                 1                   2                       0
## 45                 0                   2                       1
## 46                 3                   1                       1
## 47                 1                   2                       1
## 48                 1                   5                       0
## 49                 0                   1                       0
## 50                 0                   0                       0
##    Zanthoxylum.panamense Zanthoxylum.setulosum Zuelania.guidonia
## 1                      2                     0                 0
## 2                      2                     0                 0
## 3                      2                     0                 0
## 4                      5                     0                 1
## 5                      5                     0                 0
## 6                      3                     0                 2
## 7                      0                     0                 0
## 8                      2                     0                 0
## 9                      4                     0                 0
## 10                     4                     0                 0
## 11                     1                     0                 0
## 12                     0                     0                 0
## 13                     0                     0                 0
## 14                     1                     0                 0
## 15                     2                     0                 0
## 16                     0                     0                 0
## 17                     1                     0                 1
## 18                     1                     0                 1
## 19                     3                     0                 0
## 20                     1                     0                 0
## 21                     0                     0                 0
## 22                     1                     0                 0
## 23                     0                     0                 0
## 24                     0                     0                 0
## 25                     1                     0                 0
## 26                     0                     0                 0
## 27                     2                     0                 0
## 28                     0                     0                 1
## 29                     0                     0                 0
## 30                     3                     0                 0
## 31                     1                     0                 0
## 32                     2                     0                 0
## 33                     1                     0                 0
## 34                     3                     0                 0
## 35                     1                     0                 0
## 36                     0                     0                 0
## 37                     4                     0                 0
## 38                     1                     0                 0
## 39                     1                     0                 0
## 40                     0                     0                 0
## 41                     1                     1                 0
## 42                     1                     0                 1
## 43                     0                     0                 0
## 44                     0                     0                 0
## 45                     0                     0                 0
## 46                     1                     0                 0
## 47                     0                     0                 1
## 48                     1                     0                 2
## 49                     1                     0                 0
## 50                     2                     0                 0

Description from package

A data frame with 50 plots (rows) of 1 hectare with counts of trees on each plot with total of 225 species (columns). Full Latin names are used for tree species. The names were updated against http://www.theplantlist.org and Kress et al. (2009) which allows matching 207 of species against doi: 10.5061/dryad.63q27 (Zanne et al., 2014).

EDA

Metadata analysis

BCI.env %>% str
## 'data.frame':    50 obs. of  9 variables:
##  $ UTM.EW       : num  625754 625754 625754 625754 625754 ...
##  $ UTM.NS       : num  1011569 1011669 1011769 1011869 1011969 ...
##  $ Precipitation: int  2530 2530 2530 2530 2530 2530 2530 2530 2530 2530 ...
##  $ Elevation    : int  120 120 120 120 120 120 120 120 120 120 ...
##  $ Age.cat      : Factor w/ 2 levels "c2","c3": 2 2 2 2 2 2 2 2 2 2 ...
##  $ Geology      : Factor w/ 1 level "Tb": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Habitat      : Factor w/ 5 levels "OldHigh","OldLow",..: 3 2 2 2 3 2 2 2 2 2 ...
##  $ Stream       : Factor w/ 2 levels "No","Yes": 2 2 1 1 1 1 2 2 1 1 ...
##  $ EnvHet       : num  0.627 0.394 0 0 0.461 ...
unique(paste(BCI.env$UTM.EW, BCI.env$UTM.NS))
##  [1] "625753.967 1011568.985" "625753.967 1011668.985" "625753.967 1011768.985"
##  [4] "625753.967 1011868.985" "625753.967 1011968.985" "625853.967 1011568.985"
##  [7] "625853.967 1011668.985" "625853.967 1011768.985" "625853.967 1011868.985"
## [10] "625853.967 1011968.985" "625953.967 1011568.985" "625953.967 1011668.985"
## [13] "625953.967 1011768.985" "625953.967 1011868.985" "625953.967 1011968.985"
## [16] "626053.967 1011568.985" "626053.967 1011668.985" "626053.967 1011768.985"
## [19] "626053.967 1011868.985" "626053.967 1011968.985" "626153.967 1011568.985"
## [22] "626153.967 1011668.985" "626153.967 1011768.985" "626153.967 1011868.985"
## [25] "626153.967 1011968.985" "626253.967 1011568.985" "626253.967 1011668.985"
## [28] "626253.967 1011768.985" "626253.967 1011868.985" "626253.967 1011968.985"
## [31] "626353.967 1011568.985" "626353.967 1011668.985" "626353.967 1011768.985"
## [34] "626353.967 1011868.985" "626353.967 1011968.985" "626453.967 1011568.985"
## [37] "626453.967 1011668.985" "626453.967 1011768.985" "626453.967 1011868.985"
## [40] "626453.967 1011968.985" "626553.967 1011568.985" "626553.967 1011668.985"
## [43] "626553.967 1011768.985" "626553.967 1011868.985" "626553.967 1011968.985"
## [46] "626653.967 1011568.985" "626653.967 1011668.985" "626653.967 1011768.985"
## [49] "626653.967 1011868.985" "626653.967 1011968.985"

All positions are unique. Lets draw tham:

BCI.env %>%
  ggplot(aes(UTM.EW, UTM.NS, color = 1:50)) + 
  geom_point() +
  theme_minimal() +
  scale_color_viridis("ID")

cat("Precipitation: ", unique(BCI.env$Precipitation), "\n")
## Precipitation:  2530
cat("Elevation: ", unique(BCI.env$Elevation), "\n")
## Elevation:  120
cat("Age.cat: ", unique(BCI.env$Age.cat), "\n")
## Age.cat:  2 1
cat("Geology: ", unique(BCI.env$Geology), "\n")
## Geology:  1
cat("Habitat: ", unique(BCI.env$Habitat), "\n")
## Habitat:  3 2 4 1 5
cat("Stream: ", unique(BCI.env$Stream), "\n")
## Stream:  2 1
cat("EnvHet: ", unique(BCI.env$EnvHet), "\n")
## EnvHet:  0.6272 0.3936 0 0.4608 0.0768 0.3808 0.2112 0.4032 0.6624 0.1472 0.6592 0.2688 0.624 0.4352 0.608 0.3648 0.3328 0.6528 0.6144 0.4928 0.7264 0.6208 0.5568 0.3424 0.4992 0.6368

Precipitation, elevation and geology is the same for all samples. So it is worth to exclude them

BCI.env <- BCI.env[,-c(3,4,6)]

Visualize all other distributions:

## Warning in geom_histogram(aes(Age.cat), stat = "count", show.legend = F, :
## Ignoring unknown parameters: `binwidth`, `bins`, and `pad`
## Warning in geom_histogram(aes(Habitat), stat = "count", show.legend = F, :
## Ignoring unknown parameters: `binwidth`, `bins`, and `pad`
## Warning in geom_histogram(aes(Stream), stat = "count", show.legend = F, :
## Ignoring unknown parameters: `binwidth`, `bins`, and `pad`
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Most of samples (49 out of 50) have age category c3. So it might be worth to exclude one with age category c2 to reduce the noise in samples when performing statistical transformations in future

#rmV <- which(BCI.env$Age.cat == "c2")
#BCI.env <- BCI.env[-rmV,]
#BCI <- BCI[-rmV,]

How independent are Stream,Habitat and EnvHet?

BCI.env %>%
  ggplot(aes(y = EnvHet, "", color = EnvHet)) +
  geom_beeswarm() +
  facet_grid(Stream~Habitat) +
  theme_minimal() +
  scale_color_viridis(direction = -1) +
  ylab("amount") + xlab("")

There is no samples with stream presence and several habitat parameters. Also, there is lack of swamp and young habitat samples.

Making tidy table

df <- BCI %>%
  rownames_to_column("id") %>%
  pivot_longer(cols = 2:226) %>%
  as_tibble() %>%
  mutate_at("value", as.numeric) %>%
  mutate_at(c("id", "name"), as.factor) %>%
  left_join(
    BCI.env %>%
      rownames_to_column("id"),
    by = "id")
  

df$id <- fct_inseq(df$id)

Sample analysis

df %>%
  ggplot(aes(y = id, log10(value+1), fill = id)) +
  geom_boxplot(show.legend = F, linewidth = 0.1, outliers = F) +
  geom_jitter(show.legend = F, size = 0.1, alpha = 0.1) +
  scale_fill_viridis_d() +
  theme_minimal()

Most of values are 0 or 1, so first of all lets check the amount of species per sample

df %>%
  mutate("pres" = (value > 0)/225) %>%
  summarise(pres = sum(pres), .by = c(UTM.EW, UTM.NS)) %>%
  ggplot(aes(x = UTM.EW, y = UTM.NS, fill = pres)) +
  geom_tile() +
  scale_fill_viridis("% of all species presented", direction = -1) +
  theme_minimal()

All samples are pretty consistent by amount of different species in each of them. And how about overall amount of trees?

df %>%
  summarise(N = sum(value), .by = c(UTM.EW, UTM.NS)) %>%
  ggplot(aes(x = UTM.EW, y = UTM.NS, fill = N)) +
  geom_tile() +
  scale_fill_viridis("trees", direction = -1) +
  theme_minimal() +
  theme(legend.position = "bottom")

What is the variance behind this values?

g1 <- df %>%
  summarise(N = sum(value), .by = c(UTM.EW, UTM.NS)) %>%
  ggplot(aes(x = N)) +
  geom_density() +
  xlab("number of trees") + ylab("density") +
  scale_fill_viridis() +
  theme_minimal()

g2 <- df %>%
  mutate("pres" = (value > 0)/225) %>%
  summarise(pres = sum(pres), .by = c(UTM.EW, UTM.NS)) %>%
  ggplot(aes(x = pres)) +
  geom_density() +
  xlab("presence of trees") + ylab("") +
  scale_fill_viridis() +
  theme_minimal()

ggarrange(g1, g2, nrow = 1)

All samples are pretty normal by trees overall presence, but one sample is with excepted amount of trees. Lets explore it:

tmp <- df %>% 
  summarise(N = sum(value), .by = id)

tmp <- tmp$id[tmp$N > 550] %>% as.character
top <- df[df$id == tmp, c("value", "name")]
top <- top$name[order(top$value, decreasing = T)][1:20]

df %>%
  summarise(value = mean(value), id = "mean", .by = name) %>%
  rbind(df[df$id == tmp, c("value", "name", "id")]) %>%
  subset(name %in% top) %>%
  ggplot(aes(value, fct_reorder(name,value), fill = id)) +
  geom_col(position = "dodge") +
  theme_minimal() + ylab("species")

The biggest differences occurce because of exceptionally high level of Gustavia superba and Alsesis blackania. It is better to remove this sample in future Q-mode analysis

BTW, while adjusting nice legend I suddenly revealed a true masterpiece

df %>%
  summarise(N = sum(value), .by = c(UTM.EW, UTM.NS)) %>%
  ggplot(aes(x = N, color = N)) +
  geom_segment(aes(yend = 0, xend = ..density..), stat = "density") +
  xlab("density") + ylab("") +
  scale_fill_viridis() +
  theme_minimal()
## Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(density)` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: The following aesthetics were dropped during statistical transformation:
## colour.
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

We can see that in the center there are less trees, than on the north east periphery. The amount of trees does not seems to correlate to their diversity.

So, in this way I perform some R-mode analysis. And what about Q-mode analysis? Is it better to use normalized data for the process? Possible yes, but let’s check it

Species analysis

sum_sample <- df %>% summarise(total = sum(value), .by = c(id))

df <- df %>%
  left_join(sum_sample, by = "id") %>%
  mutate("am" = value/total)

Let’s check, what is better to use in further standartization process

sum_tree1 <- df %>% summarise(mt = mean(value), 
                              st = sd(value),
                              .by = c(name))

sum_tree2 <- df %>% summarise(mt = mean(am), 
                              st = sd(am),
                              .by = c(name))

Mean visualization

Standardized using absolute value

sum_tree <- sum_tree1[order(sum_tree1$mt),]
sum_tree$name <- fct_inorder(sum_tree$name)

sum_tree %>%
  mutate(vmax = mt + st) %>%
  mutate(vmin = ifelse(mt - st > 0, mt - st, 0)) %>%
  ggplot(aes(y = name, mt, color = name, text = name)) +
  geom_pointrange(aes(xmin = vmin, xmax = vmax), 
                  show.legend = F, size = 0.1, alpha = 0.2) +
  theme_minimal() +
  ylab("species") +
  theme(panel.grid.minor.y = element_blank(),
        panel.grid.major.y = element_blank(),
        axis.text.y = element_blank()) +
  scale_color_viridis_d(direction = -1) +
  xlab("number")

Standardized using relative amount in sample

sum_tree <- sum_tree2[order(sum_tree2$mt),]
sum_tree$name <- fct_inorder(sum_tree$name)

sum_tree %>%
  mutate(vmax = mt + st) %>%
  mutate(vmin = ifelse(mt - st > 0, mt - st, 0)) %>%
  ggplot(aes(y = name, mt, color = name, text = name)) +
  geom_pointrange(aes(xmin = vmin, xmax = vmax), 
                  show.legend = F, size = 0.1, alpha = 0.2) +
  theme_minimal() +
  ylab("species") +
  theme(panel.grid.minor.y = element_blank(),
        panel.grid.major.y = element_blank(),
        axis.text.y = element_blank()) +
  scale_color_viridis_d(direction = -1) +
  xlab("amount")

Using absolute values might be slightly better

Values vizualization

Is the real values normally distribured across all species?

df <- df %>%
  left_join(sum_tree1, by = "name")

ggplot(df, aes(am)) +
  geom_jitter(aes(color = mt, y = 200), height = 200, size = 0.1) +
  geom_density(color = "red") +
  scale_color_viridis("mean per species", direction = -1) +
  theme_minimal() +
  ylab("density")

I can’t hold on beyond using beeswarm here)

ggplot(df[df$value!=0,], aes(am, y = "", color = name)) +
  geom_beeswarm(show.legend = F, size = 0.2) +
  theme_minimal() +
  scale_color_viridis_d()

One really bad outlier with the exceptional amount of one tree (35) might not be used in further sample analysis, as well as the 33rd sample with c2

Full analysis

Let’s check independence of influencing factors:

ggplot(df[df$am!=0,], aes(y = am, "", color = EnvHet)) +
  geom_beeswarm(size = 0.5, alpha = 0.5) +
  facet_grid(Stream~Habitat) +
  theme_minimal() +
  scale_color_viridis(direction = -1) +
  ylab("amount") + xlab("")

Seems that for further Q-mode analysis is also better to exclude all young samples because of outliers. Also, swamp, young habitats and samples with presence of stream have high environmental heterogenity. So, env.het is a type of habitat measure..

Let’s move on!

NMDS

Let’s use Bray-Curtis distance

NMDS <- metaMDS(BCI, k = 2, dist = "bray", autotransform = FALSE)
## Run 0 stress 0.1741506 
## Run 1 stress 0.1741506 
## ... Procrustes: rmse 3.324596e-05  max resid 0.0002059128 
## ... Similar to previous best
## Run 2 stress 0.1792031 
## Run 3 stress 0.2012435 
## Run 4 stress 0.1900287 
## Run 5 stress 0.199913 
## Run 6 stress 0.1880655 
## Run 7 stress 0.1880657 
## Run 8 stress 0.1855482 
## Run 9 stress 0.1871092 
## Run 10 stress 0.178791 
## Run 11 stress 0.1741506 
## ... Procrustes: rmse 2.611141e-05  max resid 0.0001658493 
## ... Similar to previous best
## Run 12 stress 0.224473 
## Run 13 stress 0.183808 
## Run 14 stress 0.1741506 
## ... New best solution
## ... Procrustes: rmse 3.509224e-06  max resid 1.405608e-05 
## ... Similar to previous best
## Run 15 stress 0.1997638 
## Run 16 stress 0.1741506 
## ... Procrustes: rmse 5.281221e-06  max resid 2.250866e-05 
## ... Similar to previous best
## Run 17 stress 0.1921145 
## Run 18 stress 0.1838079 
## Run 19 stress 0.1863736 
## Run 20 stress 0.1741506 
## ... Procrustes: rmse 5.457219e-06  max resid 2.16105e-05 
## ... Similar to previous best
## *** Best solution repeated 3 times
stressplot(NMDS)

A lot of data, so looks good ## Plain

ordiplot(NMDS,type = "n")
orditorp(NMDS, display="species", labels = " ", col = "#00297a70", cex = 0.2, pch = 1)
orditorp(NMDS, display="sites",labels = " ",col = "#007a3270", cex = 0.2, pch = 10)

## Add legend

Env.Het

ordiplot(NMDS,type = "n")

ordisurf(NMDS,BCI.env$EnvHet,main="",col="forestgreen", cex = 0.2)
## 
## Family: gaussian 
## Link function: identity 
## 
## Formula:
## y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
## 
## Estimated degrees of freedom:
## 3.1  total = 4.1 
## 
## REML score: 0.1980068
orditorp(NMDS, display="species", labels = " ", col = "#00297a70", cex = 0.1, pch = 1)

### Stream

tmp <- BCI.env$Stream %>% factor
cols <- match(tmp, levels(tmp), 1:length(levels(tmp)))

ordiplot(NMDS,type = "n")
ordiellipse(NMDS,BCI.env$Stream,main="",cex = 0.2, col = c("darkgreen", "darkred"))
orditorp(NMDS, display="sites",labels = " ",col = cols, cex = 0.2, pch = 10)

Stream presented samples are on the periphery of the NMDS, but does not form special group

Habitat

tmp <- BCI.env$Habitat %>% factor
cols <- match(tmp, levels(tmp), 1:length(levels(tmp)))

ordiplot(NMDS,type = "n")
ordiellipse(NMDS,BCI.env$Habitat,main="",cex = 0.2, col = c("darkgreen", "darkred"))
## Warning in chol.default(cov, pivot = TRUE): the matrix is either rank-deficient
## or not positive definite

## Warning in chol.default(cov, pivot = TRUE): the matrix is either rank-deficient
## or not positive definite

Habitats vary a little, so we can see there the influence of this factor.

NMDS_sm <- data.frame(BCI.env, scores(NMDS, display = "sites"))
NMDS_sp <- data.frame(scores(NMDS, display = "species"))

ggplot2

g1 <-  ggplot() +
  geom_point(data = NMDS_sm, aes (x = NMDS1, y = NMDS2, text = 1:50,
             colour = Habitat, shape = Stream, size = EnvHet), alpha = 0.5) +
  theme_minimal() +
  scale_color_viridis_d()
## Warning in geom_point(data = NMDS_sm, aes(x = NMDS1, y = NMDS2, text = 1:50, :
## Ignoring unknown aesthetics: text
g1

#ggplotly(g1)

Seems like 3 clusters (or 2 with outliers) with unknown properties.

What about species? Let’s annotate them by presence in samples

pres <- df %>%
  summarise(presence = sum(value > 0)/50, .by = name)

g2 <- NMDS_sp %>%
  rownames_to_column("name") %>%
  left_join(pres, by = "name") %>%
  ggplot(aes(x = NMDS1, y = NMDS2, text = name, color = presence)) +
  geom_point(alpha = 0.5, size = 0.7) +
  theme_minimal() +
  scale_color_viridis("presence", direction = -1)
  
ggplotly(g2)

As it could be predicted, low frequency trees are outliers on NMDS

Adding environmental parameters

ef <- envfit(NMDS, BCI.env)
ef$vectors %>% print
##           NMDS1    NMDS2     r2 Pr(>r)    
## UTM.EW -0.17490  0.98459 0.7548  0.001 ***
## UTM.NS  0.88876 -0.45836 0.0255  0.531    
## EnvHet -0.16403  0.98646 0.0131  0.732    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
cat("----\n")
## ----
ef$factors %>% print
## Centroids:
##                   NMDS1   NMDS2
## Age.catc2        0.1048  0.1077
## Age.catc3       -0.0021 -0.0022
## HabitatOldHigh   0.1831  0.1558
## HabitatOldLow   -0.0004 -0.0574
## HabitatOldSlope -0.2717  0.0330
## HabitatSwamp     0.3630 -0.2911
## HabitatYoung     0.5401  0.2154
## StreamNo         0.0140  0.0116
## StreamYes       -0.0859 -0.0714
## 
## Goodness of fit:
##             r2 Pr(>r)    
## Age.cat 0.0044  0.797    
## Habitat 0.4903  0.001 ***
## Stream  0.0195  0.405    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999

Habitat fits awesome the differences in data, while other parameters seems to be not correlated with samples tree amounts. Interestingly, horizontal axis UTM.EW also influence on sample properties.

Visualization:

env <- BCI.env
env[,3:5] <- env[,3:5] %>% sapply(match,
                                  env[,3:5] %>% unlist %>% factor %>% levels,
                                  1:9)

par(mfrow = c(2, 3))
o1 <- ordisurf(NMDS, env$UTM.EW, method = "REML")
o2 <- ordisurf(NMDS, env$UTM.NS, method = "REML")
o3 <- ordisurf(NMDS, env$Habitat, method = "REML")
o4 <- ordisurf(NMDS, env$Stream, method = "REML")
o5 <- ordisurf(NMDS, env$EnvHet, method = "REML")
par(mfrow = c(1, 1))

1st NMDS axis is mostly UTM.EW, while 2nd is mostly Habitat explained.

cat("UTM.EW:")
## UTM.EW:
o1 %>% summary %>% print
## 
## Family: gaussian 
## Link function: identity 
## 
## Formula:
## y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
## 
## Parametric coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 626203.97      17.67   35445   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Approximate significance of smooth terms:
##            edf Ref.df     F p-value    
## s(x1,x2) 6.077      9 23.92  <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## R-sq.(adj) =  0.815   Deviance explained = 83.8%
## -REML = 316.05  Scale est. = 15606     n = 50
cat("\n#########################\n\n")
## 
## #########################
cat("Habitat:")
## Habitat:
o3 %>% summary %>% print
## 
## Family: gaussian 
## Link function: identity 
## 
## Formula:
## y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
## 
## Parametric coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  4.28000    0.09976    42.9   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Approximate significance of smooth terms:
##            edf Ref.df     F  p-value    
## s(x1,x2) 6.407      9 3.952 7.45e-05 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## R-sq.(adj) =  0.421   Deviance explained = 49.6%
## -REML = 61.473  Scale est. = 0.4976    n = 50

Fortifying objects:

NMDS_ef <- fortify(ef)

fortify_ordisurf <- function(model) {
  xy <- expand.grid(x = model$grid$x, y = model$grid$y)
  xyz <- cbind(xy, c(model$grid$z))
  names(xyz) <- c("x", "y", "z")
  return(na.omit(xyz))
}

NMDS_os_EW <- fortify_ordisurf(o1)
NMDS_os_Habitat <- fortify_ordisurf(o3)

Let’s check real features correlation

g1 <- NMDS_sm %>%
  ggplot(aes(UTM.EW, NMDS2, color = NMDS1)) +
  geom_smooth(alpha = 0.1, color = "red", linetype = 2, method = "lm") +
  geom_point() +
  theme_minimal() +
  theme(legend.position = "bottom") +
  scale_color_viridis("NMDS1")

g2 <- NMDS_sm %>%
  ggplot(aes(Habitat, NMDS1, color = NMDS2)) +
  geom_boxplot(alpha = 0.1, aes(fill = Habitat), show.legend = F) +
  geom_beeswarm() +
  theme_minimal() +
  scale_color_viridis("NMDS2") +
  theme(legend.position = "bottom") +
  scale_fill_viridis_d()

ggarrange(g1,g2, nrow = 1)
## `geom_smooth()` using formula = 'y ~ x'
## Warning: The following aesthetics were dropped during statistical transformation:
## colour.
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

Plots can say more than me)

Visualize altogether

gg <- ggplot() +
  geom_point(data = NMDS_sm, 
             aes (x = NMDS1, y = NMDS2, 
             shape = Habitat), alpha = 0.5) +
  stat_contour(data = NMDS_os_EW, aes(x = x, y = y, z = z, colour = ..level..)) +
  geom_segment(data = NMDS_ef[6:10,],
               colour = "blue", size = 0.5, linewidth = 0.25,
               aes(x = 0, xend = NMDS1, y = 0, yend = NMDS2, text = label),
               arrow = arrow(length = unit(0.25, "cm"))) +
  labs(x = "NMDS1", y = "NMDS2") +
  theme_minimal() +
  scale_color_viridis("Coordinate, western") +
  coord_fixed()
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning in geom_segment(data = NMDS_ef[6:10, ], colour = "blue", size = 0.5, :
## Ignoring unknown aesthetics: text
ggplotly(gg)

Now we can finally postulate presence of 3 samples groups: western OldLow+OldSlope groups, OldHigh + central and eastern OldLow+OldSlope, and swamp+outliers.

So, the main features, influencing on samples are habitat and their eastern-western position.